东江氨氮污染河段的微生物群落特征
|
摘要
随着社会经济的快速发展，氮化物在环境中排放量日益提高，江河中氮化物的含量也相应增多，使水体氮收支严重失衡，进而导致近海海域水体富营养化、发生大面积赤潮。东江是华南经济最活跃地区的重要饮用水水源，其污染程度与所处地区的经济发展速度直接相关，氨氮超标现象十分普遍。河流污染既制约了社会经济的发展，也威胁了人类的健康。因此，如何加速河流微生物介导的氮循环速率，有效降低水体氮素水平，缓解氮污染的危害，已经引起了公众的广泛关注，成为当前亟待解决的环境问题。本论文针对东江氨氮污染问题，采用免培养微生物分子生态学研究方法和多变量统计分析方法相结合，研究东江氨氮污染程度不同的河段中的微生物群落组成多样性、时空变化规律，以及与环境因子之间的相关性，分析微生物群落在河流氨氮污染净化中的响应，以及影响微生物群落结构及其功能活性特征的主要因素。
通过细菌16S rRNA基因克隆建库分析，发现东江水体中浮游细菌具有广泛的多样性，包括代表性的α-变形杆菌（Alphaproteobacteria）、β-变形杆菌（Betaproteobacteria）、γ-变形杆菌（Gammaproteobacteria）、放线菌（Actinobacteria）、拟杆菌（Bacteriodetes）、疣微菌（Verrucomicrobia）和候选分类TM7。浮游细菌主要是变形杆菌（占85%）；β-变形杆菌（Betaproteobacteria）亚门的多样性和丰度分布都具有绝对的优势，如丛毛单胞菌（Comamonadaceae）在克隆库中占比例为32.0-46.7%。大多数序列（58.9%）分类到39属，其中Curvibacter、Hydrogenophaga、Polynucleobacter等菌属在东江水体中分布比较普遍。对克隆文库微生物群落组成的典范对应分析（CCA）结果表明，氨氮和硝酸盐氮等营养成份对东江微生物群落组成多样性和丰度分布有较强的影响。
应用变性梯度凝胶电泳（DGGE）技术研究不同水期的微生物群落演替。DGGE图谱及分析结果表明东江水体微生物群落在时空分布上存在动态的变化。DGGE图谱分析结果表明东江水体微生物群落结构复杂，在时空分布上存在动态的变化。条带切胶回收的序列分析也揭示了微生物的多样性组成，且大多数的微生物依然是变形杆菌，但不同采样点间的微生物组成和丰度之间存在相似性不同。非度量多维标度（MDS）结果显示丰水期与枯水期的微生物群落在聚类上明显分开，CCA分析揭示了微生物群落的动态变化与环境因子硝酸盐氮和pH的变化有较强的相关性。此外，与16S rRNA基因克隆建库分析方法进行比较，发现DGGE反映的群落信息与克隆建库的不存在明显的差异，表明DGGE作为一种快速、直观的方法，在一定程度上可以代替克隆建库方法用于研究微生物群落的多样性动态变化。
通过研究氮循环的第一个限速步骤氨氧化过程，首次发现了淡水河流东江水体里存在氨氧化古菌（AOA）。amoA基因的系统发育分析表明东江AOA为淡水泉古菌，明显不同于来源于海洋和土壤的AOA；多样性分析表明，AOA分为3个类群，占绝对优势的类群是Freshwater Cluster1cluster，在所有序列中的比例高达88%。而氨氧化细菌（AOB）主要为亚硝化单胞菌属（Nitrosomonas）和亚硝化螺菌属(Nitrosospira)两大类群；其中亚硝化单胞菌属（Nitrosomonas）数量最多，亚硝化螺菌属(Nitrosospira)则数量极少。通过定量PCR对amoA基因进行分析，东江AOA的丰度远高于AOB，且AOA/AOB的比率与氨氮污染程度呈一定的负相关性，表明东江淡水AOA比AOB具有更好的适应能力；同时也提示了AOA在东江水体氨循环中可能起着重要的作用。
本论文开展了东江微生物群落特征及其对环境因子变化的响应研究，为进一步为开发和利用东江微生物资源、更好地发挥微生物在河流污染净化和健康状况监测等方面提供重要科学数据，对控制东江水质氮污染的蔓延、加剧，保护东江河流水体的生态健康，具有重要的环境保护和社会经济意义。
With the rapid development of social economy, reactive nitrogen released into theenvironment is increasing, which results in the elevated nitrogen in rivers, subsequentlyinterferes with the balance of the nitrogen budget, even attribute to the eutrophication andbloom in a large area of red tide in coastal region. The Dongjiang river, an important rawwater for drinking water supply in South China, is contaminated by high level ammonia in thewater, and the water quality contamination is closely relate with the economic development.Due to the polluted river is not good for the economic development and threaten to humanhealth, therefore, wide public concern is focusing on the problems that how to speed up themicrobial mediated nitrogen cycling rate for effectively reducing the nitrogen level and forrelieving the risk of nitrogen pollution in the river. To exploit the solution to the nitrogencontamination, the culture-independent molecular microbial ecology methods andmultivariate statistical analysis methods were combined to study: the composition and theirdynamic changes of microbial community over spatio-temporal scale, the correlation betweenenvironmental factors and microbial community, the response of microbial communities tothe nitrogen concentration in the river and the key factors affect the activity of microbialcommunity structure.
The sequences analysis of the clone library for bacterial16S rRNA genes showed that ahigh diversity of bacterioplankton community in the Dongjiang River. Five representativephyla, including Proteobacteria (Alphaproteobacteria, Betaproteobacteria andGammaproteobacteria), Actinobacteria, Bacteriodetes, Verrucomicrobia and candidatedivision TM7, were identified in sampling sites. Most of the sequences (85.0%) wereaffiliated with the phylum of Proteobacteria, and the Betaproteobacteria was the dominantsub-phylum. and the most abundant family was Comamonadaceae with the range from32.0%to46.7%in the libraries. Most sequences (58.9%of the total) belong to39genera, and themost commonly found species were related to the genera Curvibacter, Hydrogenophaga andPolynucleobacter. The canonical correspondence analysis (CCA) ordinations of the microbialpatterns and environmental variables demonstrated that N nutrient (nitrateand ammonia) wasstrongly correlated with most bacterial communities in the Dongjiang River.
Denaturing gradient gel electrophoresis (DGGE) technique was applied to monitoringthe dynamic changes of microbial communities on the spatio-temporal scale. DGGE profilesand their digital information revealed the diversity and the variability of band patternsbetween the sampling sites in wet season and dry season. Sequences retrieved from gels evidenced the complexity of microbial community, with the dominance of phylumproteobacteria. Non-metric multidimensional scaling (MDS) revealed clear seasonalseparation based on the samples from different seasons; and CCA ordination plots revealedthat nitrate and pH were the main factors affecting the composition of bacterioplanktoncommunity. In addition, there were no significant difference between the DGGE techniqueand clone library construction method, considering the laborious and time-consumingcharacteristics of clone library construction method DGGE technique may be a more rapidand straightforward alternative choice for tracking genotypic community changes and cangive a good microbial overview with medium phylogenetic resolution in the Dongjiang River.
Ammonia-oxidizing archaea (AOA) was found firstly in the Dongjiang River throughthe molecular determination of the amoA gene, which codes the catalytic alpha-subunit ofammonia monooxygenase catalyzing the first rate-limiting step in the nitrogen cycle.Phylogenetic analysis of archaeal amoA gene revealed that AOAin the Dongjiang River wasaffiliated with Crenarchaeota, and showed lower similarity to sequences from marineenvironments and soil habitats. AOAs were divided into three clusters, and the freshwatercluster1(88%) was predominant over the other two clusters in whole basin. The AOBs weregrouped in Nitrosomonas and Nitrosospira, and Nitrosomonas was predominated overNitrosospira. The results of quantitative PCR analysis illustrated thatArchaeal amoA genesoutnumbered bacterial amoA genes in the whole basin, and the ratio ofAOA/AOB wasnegatively correlated with the ammonia concentration. These results suggested that AOAswere well adapted to the low ammonia environment and contributed to the nitrogen cycling ina relative low-ammonia habitat.
To our knowledge, the molecular analysis of the microbial community composition andtheir response to environmental factors was first report in the Dongjiang River. This study wasproviding the fundamental scientific data for the further development and utilization ofmicrobial resources, for the water purification and health status monitoring in the DongjiangRiver. Furthermore, it is of significance in the control of the nitrogen contamination and themaintaining of the river ecosystem health in the future.
通过细菌16S rRNA基因克隆建库分析，发现东江水体中浮游细菌具有广泛的多样性，包括代表性的α-变形杆菌（Alphaproteobacteria）、β-变形杆菌（Betaproteobacteria）、γ-变形杆菌（Gammaproteobacteria）、放线菌（Actinobacteria）、拟杆菌（Bacteriodetes）、疣微菌（Verrucomicrobia）和候选分类TM7。浮游细菌主要是变形杆菌（占85%）；β-变形杆菌（Betaproteobacteria）亚门的多样性和丰度分布都具有绝对的优势，如丛毛单胞菌（Comamonadaceae）在克隆库中占比例为32.0-46.7%。大多数序列（58.9%）分类到39属，其中Curvibacter、Hydrogenophaga、Polynucleobacter等菌属在东江水体中分布比较普遍。对克隆文库微生物群落组成的典范对应分析（CCA）结果表明，氨氮和硝酸盐氮等营养成份对东江微生物群落组成多样性和丰度分布有较强的影响。
应用变性梯度凝胶电泳（DGGE）技术研究不同水期的微生物群落演替。DGGE图谱及分析结果表明东江水体微生物群落在时空分布上存在动态的变化。DGGE图谱分析结果表明东江水体微生物群落结构复杂，在时空分布上存在动态的变化。条带切胶回收的序列分析也揭示了微生物的多样性组成，且大多数的微生物依然是变形杆菌，但不同采样点间的微生物组成和丰度之间存在相似性不同。非度量多维标度（MDS）结果显示丰水期与枯水期的微生物群落在聚类上明显分开，CCA分析揭示了微生物群落的动态变化与环境因子硝酸盐氮和pH的变化有较强的相关性。此外，与16S rRNA基因克隆建库分析方法进行比较，发现DGGE反映的群落信息与克隆建库的不存在明显的差异，表明DGGE作为一种快速、直观的方法，在一定程度上可以代替克隆建库方法用于研究微生物群落的多样性动态变化。
通过研究氮循环的第一个限速步骤氨氧化过程，首次发现了淡水河流东江水体里存在氨氧化古菌（AOA）。amoA基因的系统发育分析表明东江AOA为淡水泉古菌，明显不同于来源于海洋和土壤的AOA；多样性分析表明，AOA分为3个类群，占绝对优势的类群是Freshwater Cluster1cluster，在所有序列中的比例高达88%。而氨氧化细菌（AOB）主要为亚硝化单胞菌属（Nitrosomonas）和亚硝化螺菌属(Nitrosospira)两大类群；其中亚硝化单胞菌属（Nitrosomonas）数量最多，亚硝化螺菌属(Nitrosospira)则数量极少。通过定量PCR对amoA基因进行分析，东江AOA的丰度远高于AOB，且AOA/AOB的比率与氨氮污染程度呈一定的负相关性，表明东江淡水AOA比AOB具有更好的适应能力；同时也提示了AOA在东江水体氨循环中可能起着重要的作用。
本论文开展了东江微生物群落特征及其对环境因子变化的响应研究，为进一步为开发和利用东江微生物资源、更好地发挥微生物在河流污染净化和健康状况监测等方面提供重要科学数据，对控制东江水质氮污染的蔓延、加剧，保护东江河流水体的生态健康，具有重要的环境保护和社会经济意义。
With the rapid development of social economy, reactive nitrogen released into theenvironment is increasing, which results in the elevated nitrogen in rivers, subsequentlyinterferes with the balance of the nitrogen budget, even attribute to the eutrophication andbloom in a large area of red tide in coastal region. The Dongjiang river, an important rawwater for drinking water supply in South China, is contaminated by high level ammonia in thewater, and the water quality contamination is closely relate with the economic development.Due to the polluted river is not good for the economic development and threaten to humanhealth, therefore, wide public concern is focusing on the problems that how to speed up themicrobial mediated nitrogen cycling rate for effectively reducing the nitrogen level and forrelieving the risk of nitrogen pollution in the river. To exploit the solution to the nitrogencontamination, the culture-independent molecular microbial ecology methods andmultivariate statistical analysis methods were combined to study: the composition and theirdynamic changes of microbial community over spatio-temporal scale, the correlation betweenenvironmental factors and microbial community, the response of microbial communities tothe nitrogen concentration in the river and the key factors affect the activity of microbialcommunity structure.
The sequences analysis of the clone library for bacterial16S rRNA genes showed that ahigh diversity of bacterioplankton community in the Dongjiang River. Five representativephyla, including Proteobacteria (Alphaproteobacteria, Betaproteobacteria andGammaproteobacteria), Actinobacteria, Bacteriodetes, Verrucomicrobia and candidatedivision TM7, were identified in sampling sites. Most of the sequences (85.0%) wereaffiliated with the phylum of Proteobacteria, and the Betaproteobacteria was the dominantsub-phylum. and the most abundant family was Comamonadaceae with the range from32.0%to46.7%in the libraries. Most sequences (58.9%of the total) belong to39genera, and themost commonly found species were related to the genera Curvibacter, Hydrogenophaga andPolynucleobacter. The canonical correspondence analysis (CCA) ordinations of the microbialpatterns and environmental variables demonstrated that N nutrient (nitrateand ammonia) wasstrongly correlated with most bacterial communities in the Dongjiang River.
Denaturing gradient gel electrophoresis (DGGE) technique was applied to monitoringthe dynamic changes of microbial communities on the spatio-temporal scale. DGGE profilesand their digital information revealed the diversity and the variability of band patternsbetween the sampling sites in wet season and dry season. Sequences retrieved from gels evidenced the complexity of microbial community, with the dominance of phylumproteobacteria. Non-metric multidimensional scaling (MDS) revealed clear seasonalseparation based on the samples from different seasons; and CCA ordination plots revealedthat nitrate and pH were the main factors affecting the composition of bacterioplanktoncommunity. In addition, there were no significant difference between the DGGE techniqueand clone library construction method, considering the laborious and time-consumingcharacteristics of clone library construction method DGGE technique may be a more rapidand straightforward alternative choice for tracking genotypic community changes and cangive a good microbial overview with medium phylogenetic resolution in the Dongjiang River.
Ammonia-oxidizing archaea (AOA) was found firstly in the Dongjiang River throughthe molecular determination of the amoA gene, which codes the catalytic alpha-subunit ofammonia monooxygenase catalyzing the first rate-limiting step in the nitrogen cycle.Phylogenetic analysis of archaeal amoA gene revealed that AOAin the Dongjiang River wasaffiliated with Crenarchaeota, and showed lower similarity to sequences from marineenvironments and soil habitats. AOAs were divided into three clusters, and the freshwatercluster1(88%) was predominant over the other two clusters in whole basin. The AOBs weregrouped in Nitrosomonas and Nitrosospira, and Nitrosomonas was predominated overNitrosospira. The results of quantitative PCR analysis illustrated thatArchaeal amoA genesoutnumbered bacterial amoA genes in the whole basin, and the ratio ofAOA/AOB wasnegatively correlated with the ammonia concentration. These results suggested that AOAswere well adapted to the low ammonia environment and contributed to the nitrogen cycling ina relative low-ammonia habitat.
To our knowledge, the molecular analysis of the microbial community composition andtheir response to environmental factors was first report in the Dongjiang River. This study wasproviding the fundamental scientific data for the further development and utilization ofmicrobial resources, for the water purification and health status monitoring in the DongjiangRiver. Furthermore, it is of significance in the control of the nitrogen contamination and themaintaining of the river ecosystem health in the future.
引文
[1] Pesce SF, Wunderlin DA. Use of water quality indices to verify the impact of Cordoba City(Argentina) on Suquia River[J]. Water Research,2000,34(11):2915-2926.
[2] Karr JR, Chu EW. Sustaining living rivers[J]. Hydrobiologia,2000,422:1-14.
[3] Davis NM, Weaver V, Parks K, et al. An assessment of water quality, physical habitat, andbiological integrity of an urban stream in Wichita, Kansas, prior to restoration improvements(phase I)[J]. Archives of Environmental Contamination and Toxicology,2003,44(3):351-359.
[4] Magdaleno A, Puig A, de Cabo L, et al. Water pollution in an urban Argentine river[J].Bulletin of Environmental Contamination and Toxicology,2001,67(3):408-415.
[5]中华人民共和国水利部,《2008年中国水质量资源年报》,http://www.hydroinfo.gov.cn/gb/szyzlnb/.
[6]中华人民共和国环境保护部,2009年中国环境状况公报[R].北京.
[7]宋巍.东江流域农村饮用水源中微生物多样性研究及水质污染现状调查[D].陕西杨凌:西北农林科技大学,2009.
[8]金辉,张虎.东江干流水质变化趋势研究[J].上海环境科学,2000,19(z1):90-92.
[9] Galloway JN, Schlesinger WH, Levy H, et al. Nitrogen fixation: anthropogenicenhancement-environmental response[J]. Global Biogeochemical Cycles,1995,9(2):235-252.
[10] Galloway JN. The global nitrogen cycle: changes and consequences[J]. Environment Pollution,1998,102:15-24.
[11]胡国臣,张清敏.地下水硝酸盐氮污染防治研究[J].胡国臣,1999,18(5):228-230.
[12]张兴昌,邵明安.侵蚀条件下土壤氮素流失对土壤和环境的影响[J].土壤与环境,2000,9(3):249-252.
[13] Howarth RW, Billen G, Swaney D, et al. Regional nitrogen budgets and riverine N&P fluxesfor the drainages to the North Atlantic Ocean: natural and human influences[J].Biogeochemistry,1996,35(1):75-139.
[14] Turner RE, Rabalais NN. Changes in Mississippi River water-quality this century[J].Bioscience,1991,41(3):140-147.
[15] Justic D, Rabalais NN, Turner RE, et al. Changes in nutrient structure of river-dominatedcoastal waters-stoichiometric nutrient balance and Its consequences[J]. Estuarine CoastalAnd Shelf Science,1995,40(3):339-356.
[16] Vitousek PM, Aber JD, Howarth RW, et al. Human alteration of the global nitrogen cycle:sources and consequences[J]. Ecological Applications,1997,7(3):737-750.
[17] Peierls BL, Caraco NF, Pace ML, et al. Human influence on river nitrogen[J]. Nature,1991,350(6317):386-387.
[18]夏星辉,周劲松,杨志峰,等.黄河流域河水氮污染分析[J].环境科学学报,2001,21(5):563-568.
[19] Mulholland PJ, Helton AM, Poole GC, et al. Stream denitrification across biomes and itsresponse to anthropogenic nitrate loading[J]. Nature,2008,452(7184):202-205.
[20] Galloway JN, Townsend AR, Erisman JW, et al. Transformation of the nitrogen cycle: recenttrends, questions, and potential solutions[J]. Science,2008,320(5878):889-892.
[21] Gruber N, Galloway JN. An Earth-system perspective of the global nitrogen cycle[J]. Nature,2008,451(7176):293-296.
[22]叶辉,许建华.饮用水中的氨氮问题[J].中国给水排水,2000,(11):31-34.
[23]李玉婷.成都驷马桥水厂源水氨氮超标的处理工艺和运行[J].铁道劳动安全卫生与环保,2008,(01):21-23.
[24] Stigter TY, Ribeiro L, Dill AMMC. Application of a groundwater quality index as anassessment and communication tool in agro-environmental policies-Two Portuguese casestudies[J]. Journal of Hydrology,2006,327(3-4):578-591.
[25] Rabalais NN. Nitrogen in aquatic ecosystems[J]. Ambio,2002,31(2):102-112.
[26]毛战坡,单保庆,彭文启,等.氮素在河流生态系统中的滞留研究进展[J].长江流域资源与环境,2006,15(4):480-484.
[27] Zehr JP. Nitrogen fixation by marine cyanobacteria[J]. Trends in Microbiology,2011,19(4):162-173.
[28] K nneke M, Bernhard AE, de la Torre JR, et al. Isolation of an autotrophicammonia-oxidizing marine archaeon[J]. Nature,2005,437(7058):543-546.
[29] Nicol GW, Schleper C. Ammonia-oxidising Crenarchaeota: important players in the nitrogencycle?[J]. Trends in Microbiology,2006,14(5):207-212.
[30] Robertson LA, Kuenen JG. Aerobic denitrification: a controversy revived[J]. Archives ofMicrobiology,1984,139(4):351-354.
[31] Patureau D, Zumstein E, Delgenes JP, et al. Aerobic denitrifiers isolated from diverse naturaland managed ecosystems[J]. Microbial Ecology,2000,39(2):145-152.
[32] Lukow T, Diekmann H. Aerobic denitrification by a newly isolated heterotrophic bacteriumstrain TL1[J]. Biotechnology Letters,1997,19(11):1157-1159.
[33] Jorgensen KS, Tiedje JM. Survival of denitrifiers in nitrate-free, anaerobic environments[J].Applied and Environmental Microbiology,1993,59(10):3297-3305.
[34] Zumft WG. Cell biology and molecular basis of denitrification[J]. Microbiology andMolecular Biology Reviews,1997,61(4):533-616.
[35] Seitzinger S, Harrison JA, Bohlke JK, et al. Denitrification across landscapes and waterscapes:a synthesis[J]. Ecological Applications,2006,16(6):2064-2090.
[36] Richards FA. Anoxic basins and fjords[M]//RIPLEY J P, SKIRROW G A. ChemicalOceanography. London; Academic Press.1965:611-645.
[37] Mulder A, Vandegraaf AA, Robertson LA, et al. Anaerobic ammonium oxidation discoveredin a denitrifying fluidized bed reactor[J]. FEMS Microbiology Ecology,1995,16(3):177-183.
[38] Strous M, Fuerst JA, Kramer EHM, et al. Missing lithotroph identified as newplanctomycete[J]. Nature,1999,400(6743):446-449.
[39] van Niftrik LA, Fuerst JA, Damste JSS, et al. The anammoxosome: an intracytoplasmiccompartment in anammox bacteria[J]. FEMS Microbiology Letters,2004,233(1):7-13.
[40] Schubert CJ, Durisch-Kaiser E, Wehrli B, et al. Anaerobic ammonium oxidation in a tropicalfreshwater system (Lake Tanganyika)[J]. Environmental Microbiology,2006,8(10):1857-1863.
[41] Zhang Y, Ruan XH, den Camp HJMO, et al. Diversity and abundance of aerobic andanaerobic ammonium-oxidizing bacteria in freshwater sediments of the Xinyi River (China)[J].Environmental Microbiology,2007,9(9):2375-2382.
[42] Strous M, Pelletier E, Mangenot S, et al. Deciphering the evolution and metabolism of ananammox bacterium from a community genome[J]. Nature,2006,440(7085):790-794.
[43] Jetten MSM, van Niftrik L, Strous M, et al. Biochemistry and molecular biology of anammoxbacteria[J]. Critical Reviews in Biochemistry and Molecular Biology,2009,44(2-3):65-84.
[44] Cotner JB, Biddanda BA. Small players, large role: Microbial influence on biogeochemicalprocesses in pelagic aquatic ecosystems[J]. Ecosystems,2002,5(2):105-121.
[45] Arrigo KR. Marine microorganisms and global nutrient cycles[J]. Nature,2005,437(7057):349-355.
[46] Francis CA, Beman JM, Kuypers MMM. New processes and players in the nitrogen cycle: themicrobial ecology of anaerobic and archaeal ammonia oxidation[J]. Isme Journal,2007,1(1):19-27.
[47] Jetten MSM, Cirpus I, Kartal B, et al.1994-2004:10years of research on the anaerobicoxidation of ammonium[J]. Biochemical Society Transactions,2005,33:119-123.
[48] den Camp HJMO, Kartal B, Guven D, et al. Global impact and application of the anaerobicammonium-oxidizing (anammox) bacteria[J]. Biochemical Society Transactions,2006,34:174-178.
[49] Penton CR, Devol AH, Tiedje JM. Molecular evidence for the broad distribution of anaerobicammonium-oxidizing bacteria in freshwater and marine sediments[J]. Applied andEnvironmental Microbiology,2006,72(10):6829-6832.
[50] Kartal B, Kuypers MMM, Lavik G, et al. Anammox bacteria disguised as denitrifiers: nitratereduction to dinitrogen gas via nitrite and ammonium[J]. Environmental Microbiology,2007,9(3):635-642.
[51] Cabello P, Roldan MD, Moreno-Vivian C. Nitrate reduction and the nitrogen cycle inarchaea[J]. Microbiology-SGM,2004,150:3527-3546.
[52] Rittmann BE, Hausner M, Loffler F, et al. A vista for microbial ecology and environmentalbiotechnology[J]. Environmental Science&Technology,2006,40(4):1096-1103.
[53] Sharma R, Ranjan R, Kapardar RK, et al."Unculturable" bacterial diversity: an untappedresource[J]. Current Science,2005,89(1):72-77.
[54] Amann RI, Ludwig W, Schleifer KH. Phylogenetic Identification and in-Situ Detection ofIndividual Microbial Cells without Cultivation[J]. Microbiological Reviews,1995,59(1):143-169.
[55]洪义国,孙谧,张云波,等.16S rRNA在海洋微生物系统分子分类鉴定及分子检测中的应用[J].海洋水产研究,2002,(01):58-63.
[56] Amann RI, Ludwig W, Schleifer KH. Phylogenetic Identification and in-Situ Detection ofIndividual Microbial-Cells without Cultivation[J]. Microbiological Reviews,1995,59(1):143-169.
[57] Hahn D, Amann RI, Ludwig W, et al. Detection of micro-organisms in soil after insituhybridization with ribosomal RNA-targeted, fluorescently labeled oligonucleotides[J]. Journalof General Microbiology,1992,138:879-887.
[58] Moter A, Gobel UB. Fluorescence in situ hybridization (FISH) for direct visualization ofmicroorganisms[J]. Journal of Microbiological Methods,2000,41(2):85-112.
[59] Gulledge J, Ahmad A, Steudler PA, et al. Family-and genus-level16S rRNA-targetedoligonucleotide probes for ecological studies of methanotrophic bacteria[J]. Applied andEnvironmental Microbiology,2001,67(10):4726-4733.
[60] Felske A, Akkermans ADL. Prominent occurrence of ribosomes from an uncultured bacteriumof the Verrucomicrobiales cluster in grassland soils[J]. Letters in Applied Microbiology,1998,26(3):219-223.
[61] Schwieger F, Tebbe CC. A new approach to utilize PCR-single-strand-conformationpolymorphism for16s rRNA gene-based microbial community analysis[J]. Applied andEnvironmental Microbiology,1998,64(12):4870-4876.
[62] Schwieger F, Tebbe CC. Effect of field inoculation with Sinorhizobium meliloti L33on thecomposition of bacterial communities in rhizospheres of a target plant (Medicago sativa) and anon-target plant (Chenopodium album)-Linking of16S rRNA gene-based single-strandconformation polymorphism community profiles to the diversity of cultivated bacteria[J].Applied and Environmental Microbiology,2000,66(8):3556-3565.
[63] Peters S, Koschinsky S, Schwieger F, et al. Succession of microbial communities during hotcomposting as detected by PCR-single-strand-conformation polymorphism-based geneticprofiles of small-subunit rRNA genes[J]. Applied and Environmental Microbiology,2000,66(3):930-936.
[64] Tiquia SM, Ichida JM, Keener HM, et al. Bacterial community profiles on feathers duringcomposting as determined by terminal restriction fragment length polymorphism analysis of16S rDNAgenes[J].Applied Microbiology and Biotechnology,2005,67(3):412-419.
[65] Smit E, Leeflang P, Wernars K. Detection of shifts in microbial community structure anddiversity in soil caused by copper contamination using amplified ribosomal DNA restrictionanalysis[J]. FEMS Microbiology Ecology,1997,23(3):249-261.
[66] Heyndrickx M, Vauterin L, Vandamme P, et al. Applicability of combined amplified ribosomalDNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy[J]. Journalof Microbiological Methods,1996,26(3):247-259.
[67] Sette LD, Simioni KCM, Vasconcellos SP, et al. Analysis of the composition of bacterialcommunities in oil reservoirs from a southern offshore Brazilian basin[J]. Antonie VanLeeuwenhoek International Journal of General and Molecular Microbiology,2007,91(3):253-266.
[68] Osborn AM, Moore ERB, Timmis KN. An evaluation of terminal-restriction fragment lengthpolymorphism (T-RFLP) analysis for the study of microbial community structure anddynamics[J]. Environmental Microbiology,2000,2(1):39-50.
[69] Dunbar J, Ticknor LO, Kuske CR. Phylogenetic specificity and reproducibility and newmethod for analysis of terminal restriction fragment profiles of16S rRNA genes frombacterial communities[J]. Applied and Environmental Microbiology,2001,67(1):190-197.
[70] Lukow T, Dunfield PF, Liesack W. Use of the T-RFLP technique to assess spatial and temporalchanges in the bacterial community structure within an agricultural soil planted withtransgenic and non-transgenic potato plants[J]. FEMS Microbiology Ecology,2000,32(3):241-247.
[71] Myers RM, Maniatis T, Lerman LS. Detection and localization of single base changes bydenaturing gradient gel electrophoresis[J]. Methods Enzymol,1987,155:501-527.
[72] Muyzer G, Dewaal EC, Uitterlinden AG. Profiling of complex microbial populations bydenaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genescoding for16S rRNA[J]. Applied and Environmental Microbiology,1993,59(3):695-700.
[73] Simpson JM, McCracken VJ, Gaskins HR, et al. Denaturing gradient gel electrophoresisanalysis of16S ribosomal DNAamplicons to monitor changes in fecal bacterial populations ofweaning pigs after introduction of Lactobacillus reuteri strain MM53[J]. Applied andEnvironmental Microbiology,2000,66(11):4705-4714.
[74] ben Omar N, Ampe F. Microbial community dynamics during production of the Mexicanfermented maize dough pozol[J]. Applied and Environmental Microbiology,2000,66(9):3664-3673.
[75] Cocolin L, Manzano M, Cantoni C, et al. Denaturing gradient gel electrophoresis analysis ofthe16S rRNA gene V1region to monitor dynamic changes in the bacterial population duringfermentation of Italian sausages[J]. Applied and Environmental Microbiology,2001,67(11):5113-5121.
[76] Takai K, Horikoshi K. Rapid detection and quantification of members of the archaealcommunity by quantitative PCR using fluorogenic probes[J]. Applied and EnvironmentalMicrobiology,2000,66(11):5066-5072.
[77] Ochsenreiter T, Selezi D, Quaiser A, et al. Diversity and abundance of Crenarchaeota interrestrial habitats studied by16S RNA surveys and real time PCR[J]. EnvironmentalMicrobiology,2003,5(9):787-797.
[78] James FC, Mcculloch CE. Multivariate analysis in ecology and systematics: panacea orpandora box?[J]. Annual Review of Ecology and Systematics1990,21:129-166.
[79] Franklin RB, Mills AL. Multi-scale variation in spatial heterogeneity for microbial communitystructure in an eastern Virginia agricultural field[J]. FEMS Microbiology Ecology,2003,44(3):335-346.
[80] Mouser PJ, Rizzo DM, Roling WF, et al. A multivariate statistical approach to spatialrepresentation of groundwater contamination using hydrochemistry and microbial communityprofiles[J]. Environmental Science&Technology,2005,39(19):7551-7559.
[81] Terbraak CJF. Canonical correspondence analysis: a new eigenvector technique formultivariate direct gradient analysis[J]. Ecology,1986,67(5):1167-1179.
[82] Ludvigsen L, Albrechtsen HJ, Holst H, et al. Correlating phospholipid fatty acids (PLFA) in alandfill leachate polluted aquifer with biogeochemical factors by multivariate statisticalmethods[J]. FEMS Microbiology Reviews1997,20(3-4):447-460.
[83] Weckstrom J, Korhola A. Patterns in the distribution, composition and diversity of diatomassemblages in relation to ecoclimatic factors in Arctic Lapland[J]. Journal of Biogeography,2001,28(1):31-45.
[84] Boon N, De Windt W, Verstraete W, et al. Evaluation of nested PCR-DGGE (denaturinggradient gel electrophoresis) with group-specific16S rRNA primers for the analysis ofbacterial communities from different wastewater treatment plants[J]. FEMS MicrobiologyEcology,2002,39(2):101-112.
[85] Stepanauskas R, Moran MA, Bergamaschi BA, et al. Covariance of bacterioplanktoncomposition and environmental variables in a temperate delta system[J]. Aquatic MicrobialEcology,2003,31(1):85-98.
[86] Cordova-Kreylos AL, Cao YP, Green PG, et al. Diversity, composition, and geographicaldistribution of microbial communities in california salt marsh Sediments[J]. Applied andEnvironmental Microbiology,2006,72(5):3357-3366.
[87] Ikenaga M, Guevara R, Dean AL, et al. Changes in community structure of sediment bacteriaalong the Florida Coastal Everglades marsh-mangrove-seagrass salinity gradient[J]. MicrobialEcology,2010,59(2):284-295.
[88]周红,张志南.大型多元统计软件PRIMER的方法原理及其在底栖群落生态学中的应用[J].青岛海洋大学学报(自然科学版),2003,(01):58-64.
[89] Ongley E. Modernization of water quality programs in developing countries: issues ofrelevancy and cost efficiency[J]. Water Quality International,1998:37-42.
[90] Debels P, Figueroa R, Urrutia R, et al. Evaluation of water quality in the Chillan River(Central Chile) using physicochemical parameters and a modified Water Quality Index[J].Environmental Monitoring andAssessment,2005,110(1-3):301-322.
[91] Rauch W, Henze M, Koncsos L, et al. River water quality modelling: I. State of the art[J].Water Science and Technology,1998,38(11):237-244.
[92] Shanahan P, Henze M, Koncsos L, et al. River water quality modelling: II. Problems of theart[J]. Water Science and Technology,1998,38(11):245-252.
[93] Somlyody L, Henze M, Koncsos L, et al. River water quality modelling: III. Future of theart[J]. Water Science and Technology,1998,38(11):253-260.
[94] Sanchez E, Colmenarejo MF, Vicente J, et al. Use of the water quality index and dissolvedoxygen deficit as simple indicators of watersheds pollution[J]. Ecological Indicators,2007,7(2):315-328.
[95] Kannel PR, Lee S, Lee YS, et al. Application of water quality indices and dissolved oxygen asindicators for river water classification and urban impact assessment[J]. EnvironmentalMonitoring andAssessment,2007,132(1-3):93-110.
[96] Cude CG. Oregon water quality index: A tool for evaluating water quality managementeffectiveness[J]. Journal of the American Water Resources Association,2001,37(1):125-137.
[97] Liou S-M, Lo S-L, Wang S-H. Ageneralized water quality index for Taiwan[J]. EnvironmentalMonitoring andAssessment,2004,96(1):35-52.
[98] Banerjee T, Srivastava RK. Application of water quality index for assessment of surface waterquality surrounding integrated industrial estate-Pantnagar[J]. Water Science and Technology,2009,60(8):2041-2053.
[99] Chaturvedi MK, Bassin JK. Assessing the water quality index of water treatment plant andbore wells, in Delhi, India[J]. Environmental Monitoring and Assessment,2010,163(1-4):449-453.
[100] Hills P, Zhang L, Liu J. Transboundary pollution between Guangdong Province and HongKong: threats to water quality in the Pearl River Estuary and their implications forenvironmental policy and planning[J]. Journal of Environmental Planning and Management,1998,41(3):375-396.
[101] Ho KC, Hui KC. Chemical contamination of the East River (Dongjiang) and its implication onsustainable development in the Pearl River Delta[J]. Environment International,2001,26(5-6):303-308.
[102] Shuhaimi-Othman M, Lim EC, Mushrifah I. Water quality changes in Chini Lake, Pahang,West Malaysia[J]. Environmental Monitoring andAssessment,2007,131(1-3):279-292.
[103] Bellos D, Sawidis T. Chemical pollution monitoring of the River Pinios (Thessalia-Greece)[J].Journal of Environmental Management,2005,76(4):282-292.
[104]陈静生,高学民,夏星辉,等.长江水系河水氮污染[J].环境化学,1999,(04):289-293.
[105]刘国华,傅伯杰,杨平.海河水环境质量及污染物入海通量[J].环境科学,2001,(04):46-50.
[106]毛剑英,朱建平,肖建军.近年来淮河干流氮污染状况与变化趋势[J].中国环境监测,2003,19(05):41-43.
[107]刘元波,高锡芸.太湖北部梅梁湾水域水质因子聚类[J].湖泊科学,1997,9(03):255-260.
[108]朱余,王凤.巢湖流域水质状况与环境目标可达性分析[J].环境监测管理与技术,2004,16(06):22-23,26.
[109]杨文龙，杨树华.滇池流域非点源污染控制区划研究[J].云南环境科学,1996,(03).
[110] Vega M, Pardo R, Barrado E, et al. Assessment of seasonal and polluting effects on the qualityof river water by exploratory data analysis[J]. Water Research,1998,32(12):3581-3592.
[111] Winter C, Hein T, Kavka G, et al. Longitudinal changes in the bacterial communitycomposition of the Danube River: a whole-river approach[J]. Applied and EnvironmentalMicrobiology,2007,73(2):421-431.
[112] Kirchman DL, Dittel AI, Findlay SEG, et al. Changes in bacterial activity and communitystructure in response to dissolved organic matter in the Hudson River, New York[J]. AquaticMicrobial Ecology,2004,35(3):243-257.
[113] Cebron A, Berthe T, Garnier J. Nitrification and nitrifying bacteria in the lower Seine Riverand estuary (France)[J]. Applied and Environmental Microbiology,2003,69(12):7091-7100.
[114] Cebron A, Coci M, Garnier J, et al. Denaturing gradient gel electrophoretic analysis ofammonia-oxidizing bacterial community structure in the lower Seine River: impact of Pariswastewater effluents[J]. Applied and Environmental Microbiology,2004,70(11):6726-6737.
[115] Crump BC, Armbrust EV, Baross JA. Phylogenetic analysis of particle-attached andfree-living bacterial communities in the Columbia river, its estuary, and the adjacent coastalocean[J]. Applied and Environmental Microbiology,1999,65(7):3192-3204.
[116] Stevens H, Ulloa O. Bacterial diversity in the oxygen minimum zone of the eastern tropicalSouth Pacific[J]. Environmental Microbiology,2008,10(5):1244-1259.
[117] Giovannoni SJ, Britschgi TB, Moyer CL, et al. Genetic diversity in Sargasso Seabacterioplankton[J]. Nature,1990,345(6270):60-63.
[118] Fuhrman JA, Mccallum K, Davis AA. Novel major archaebacterial group from marineplankton[J]. Nature,1992,356(6365):148-149.
[119] Sekiguchi H, Koshikawa H, Hiroki M, et al. Bacterial distribution and phylogenetic diversityin the Changjiang estuary before the construction of the Three Gorges Dam[J]. MicrobialEcology,2002,43(1):82-91.
[120] Hewson I, Fuhrman JA. Richness and diversity of bacterioplankton species along an estuarinegradient in Moreton Bay, Australia[J]. Applied and Environmental Microbiology,2004,70(6):3425-3433.
[121] Stehr G, Bottcher B, Dittberner P, et al. The ammonia-oxidizing nitrifying population of theRiver Elbe estuary[J]. FEMS Microbiology Ecology,1995,17(3):177-186.
[122] Ovreas L, Forney L, Daae FL, et al. Distribution of bacterioplankton in meromictic LakeSaelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplifiedgene fragments coding for16S rRNA[J]. Applied and Environmental Microbiology,1997,63(9):3367-3373.
[123] Li SK, Xiao X, Yin XB, et al. Bacterial community along a historic lake sediment core ofArdley Island, west Antarctica[J]. Extremophiles,2006,10(5):461-467.
[124] Gaidos E, Lanoil B, Thorsteinsson T, et al. A viable microbial community in a subglacialvolcanic crater lake, Iceland[J]. Astrobiology,2004,4(3):327-344.
[125] Zwart G, Crump BC, Agterveld MPKV, et al. Typical freshwater bacteria: an analysis ofavailable16S rRNA gene sequences from plankton of lakes and rivers[J]. Aquatic MicrobialEcology,2002,28(2):141-155.
[126] B ckelmann U, Manz W, Neu TR, et al. Characterization of the microbial community of loticorganic aggregates ('river snow') in the Elbe River of Germany by cultivation and molecularmethods[J]. FEMS Microbiology Ecology,2000,33(2):157-170.
[127] Li D, Yang M, Li Z, et al. Change of bacterial communities in sediments along Songhua Riverin Northeastern China after a nitrobenzene pollution event[J]. FEMS Microbiology Ecology,2008,65(3):494-503.
[128] Battin TJ, Wille A, Sattler B, et al. Phylogenetic and functional heterogeneity of sedimentbiofilms along environmental gradients in a glacial stream[J]. Applied and EnvironmentalMicrobiology,2001,67(2):799-807.
[129] Lemke MJ, Lienau EK, Rothe J, et al. Description of freshwater bacterial assemblages fromthe upper Parana River floodpulse system, Brazil[J]. Microbial Ecology,2009,57(1):94-103.
[130] Crump BC, Peterson BJ, Raymond PA, et al. Circumpolar synchrony in big riverbacterioplankton[J]. Proceedings of the National Academy of Sciences of the United States ofAmerica,2009,106(50):21208-21212.
[131] Herfort L, Schouten S, Abbas B, et al. Variations in spatial and temporal distribution ofArchaea in the North Sea in relation to environmental variables[J]. FEMS MicrobiologyEcology,2007,62(3):242-257.
[132] Goh F, Allen MA, Leuko S, et al. Determining the specific microbial populations and theirspatial distribution within the stromatolite ecosystem of Shark Bay[J]. Isme Journal,2009,3(4):383-396.
[133] Newton RJ, Jones SE, Eiler A, et al. A guide to the natural history of freshwater lakebacteria[J]. Microbiology and Molecular Biology Reviews,2011,75(1):14-49.
[134] Crump BC, Hobbie JE. Synchrony and seasonality in bacterioplankton communities of twotemperate rivers[J]. Limnology and Oceanography,2005,50(6):1718-1729.
[135] Zehr JP, Ward BB. Nitrogen cycling in the ocean: new perspectives on processes andparadigms[J]. Applied and Environmental Microbiology,2002,68(3):1015-1024.
[136] Mason OU, Di Meo-Savoie CA, Van Nostrand JD, et al. Prokaryotic diversity, distribution,and insights into their role in biogeochemical cycling in marine basalts[J]. Isme Journal,2009,3(2):231-242.
[137]金辉.东江干流东莞段水质研究[J].环境科学研究,2001,14(3):45-48.
[138]金辉,李榴芬,朱建民.东江中游水污染状况及其变化趋势[J].广西师院学报(自然科学版),2001,18(2):60-62.
[139] Liang Y, Fung PK, Tse MF, et al. Sources and seasonal variation of PAHs in the sediments ofdrinking water reservoirs in Hong Kong and the Dongjiang River (China)[J]. Environ MonitAssess,2008,146(1-3):41-50.
[140] Delong EF, Wickham GS, Pace NR. Phylogenetic stains: ribosomal RNA-based probes for theidentification of single cells[J]. Science,1989,243(4896):1360-1363.
[141] Gurtler V, Stanisich VA. New approaches to typing and identification of bacteria using the16S-23S rDNAspacer region[J]. Microbiology,1996,142:3-16.
[142] Hall T. Biological sequence alignment editor for Win95/98/NT/2K/XP.[M]. Carlsbad, CA: IbisBiosicences,1999.
[143] Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool[J]. Journal ofMolecular Biology1990,215(3):403-410.
[144] Cole JR, Wang Q, Cardenas E, et al. The Ribosomal Database Project: improved alignmentsand new tools for rRNAanalysis[J]. Nucleic Acids Research,2009,37: D141-145.
[145] Tamura K, Dudley J, Nei M, et al. MEGA4: molecular evolutionary genetics analysis (MEGA)software version4.0[J]. Molecular Biology and Evolution,2007,24(8):1596-1599.
[146] Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetictrees[J]. Molecular Biology and Evolution,1987,4(4):406-425.
[147] Kimura M. A simple method for estimating evolutionary rates of base substitutions throughcomparative studies of nucleotide sequences[J]. J Mol Evol,1980,16(2):111-120.
[148] Chao A, Bunge J. Estimating the number of species in a Stochastic abundance model[J].Biometrics,2002,58(3):531-539.
[149] Xu M, Wu WM, Wu L, et al. Responses of microbial community functional structures topilot-scale uranium in situ bioremediation[J]. ISME J,2010,4:1060-1070.
[150] ter Braak CJF, milauer P. CANOCO reference manual and CanoDraw for Windows user'sguide: software for canonical community ordination (version4.5).[M]. Ithaca NY, USA;Microcomputer Power.2002:500.
[151] Schloss PD, Larget BR, Handelsman J. Integration of microbial ecology and statistics: a test tocompare gene libraries[J]. Applied and Environmental Microbiology,2004,70(9):5485-5492.
[152] Hahn MW, Kasalicky V, Jezbera J, et al. Limnohabitans curvus gen. nov., sp nov., a planktonicbacterium isolated from a freshwater lake[J]. International Journal of Systematic andEvolutionary Microbiology,2010,60:1358-1365.
[153] Heckmann K, Schmidt HJ. Polynucleobacter necessarius gen. nov., sp. nov., an obligatelyendosymbiotic bacterium living in the cytoplasm of Euplotes aediculatus[J]. InternationalJournal of Systematic Bacteriology,1987,37(4):456-457.
[154] Jezbera J, Jezberova J, Brandt U, et al. Ubiquity of Polynucleobacter necessarius subspeciesasymbioticus results from ecological diversification[J]. Environmental Microbiology,2011,13(4):922-931.
[155] Hiorns WD, Methe BA, NierzwickiBauer SA, et al. Bacterial diversity in AdirondackMountain lakes as revealed by16S rRNA gene sequences[J]. Applied and EnvironmentalMicrobiology,1997,63(7):2957-2960.
[156] Zwart G, Hiorns WD, Methe BA, et al. Nearly identical16S rRNA sequences recovered fromlakes in North America and Europe indicate the existence of clades of globally distributedfreshwater bacteria[J]. Systematic andApplied Microbiology,1998,21(4):546-556.
[157] Wu X, Xi WY, Ye WJ, et al. Bacterial community composition of a shallow hypertrophicfreshwater lake in China, revealed by16S rRNA gene sequences[J]. FEMS MicrobiologyEcology,2007,61(1):85-96.
[158] Newton RJ, Kent AD, Triplett EW, et al. Microbial community dynamics in a humic lake:differential persistence of common freshwater phylotypes[J]. Environmental Microbiology,2006,8(6):956-970.
[159] Simek K, Armengol J, Comerma M, et al. Changes in the epilimnetic bacterial communitycomposition, production, and protist-induced mortality along the longitudinal axis of a highlyeutrophic reservoir[J]. Microbial Ecology,2001,42(3):359-371.
[160] Simek K, Hornak K, Jezbera J, et al. Influence of top-down and bottom-up manipulations onthe R-BT065subcluster of beta-proteobacteria, an abundant group in bacterioplankton of afreshwater reservoir[J]. Applied and Environmental Microbiology,2005,71(5):2381-2390.
[161] Glockner FO, Zaichikov E, Belkova N, et al. Comparative16S rRNA analysis of lakebacterioplankton reveals globally distributed phylogenetic clusters including an abundantgroup of actinobacteria[J]. Applied and Environmental Microbiology,2000,66(11):5053-5065.
[162] Burkert U, Warnecke F, Babenzien D, et al. Members of a readily enrichedbeta-proteobacterial clade are common in surface waters of a humic lake[J]. Applied andEnvironmental Microbiology,2003,69(11):6550-6559.
[163] Hahn MW. Isolation of strains belonging to the cosmopolitan Polynucleobacter necessariuscluster from freshwater habitats located in three climatic zones[J]. Applied and EnvironmentalMicrobiology,2003,69(9):5248-5254.
[164] Head IM, Hiorns WD, Embley TM, et al. The phylogeny of autotrophic ammonia-oxidizingbacteria as determined by analysis of16s ribosomal-RNA rene-sequences[J]. Journal ofGeneral Microbiology,1993,139:1147-1153.
[165] Teske A, Hinrichs KU, Edgcomb V, et al. Microbial diversity of hydrothermal sediments in theGuaymas Basin: evidence for anaerobic methanotrophic communities[J]. Applied andEnvironmental Microbiology,2002,68(4):1994-2007.
[166] Maksimenko SY, Zemskaya TI, Pavlova ON, et al. Microbial community of the water columnof the Selenga River-Lake Baikal biogeochemical barrier[J]. Microbiology,2008,77(5):587-594.
[167] Xie CH, Yokota A. Sphingomonas azotifigens sp nov., a nitrogen-fixing bacterium isolatedfrom the roots of Oryza sativa[J]. International Journal of Systematic and EvolutionaryMicrobiology,2006,56:889-893.
[168] Warnecke F, Amann R, Pernthaler J. Actinobacterial16S rRNAgenes from freshwater habitatscluster in four distinct lineages[J]. Environmental Microbiology,2004,6(3):242-253.
[169] Sekar R, Pernthaler A, Pernthaler J, et al. An improved protocol for quantification offreshwater Actinobacteria by fluorescence in situ hybridization[J]. Applied and EnvironmentalMicrobiology,2003,69(5):2928-2935.
[170] Witzel KP, Overbeck HJ. Heterotrophic nitrification by Arthrobacter sp.(Strain9006) asinfluenced by different cultural conditions, growth state and acetate metabolism[J]. Archivesof Microbiology,1979,122(2):137-143.
[171] Brierley EDR, Wood M. Heterotrophic nitrification in an acid forest soil: isolation andcharacterisation of a nitrifying bacterium[J]. Soil Biology&Biochemistry,2001,33(10):1403-1409.
[172] Elifantz H, Malmstrom RR, Cottrell MT, et al. Assimilation of polysaccharides and glucose bymajor bacterial groups in the Delaware Estuary[J]. Applied and Environmental Microbiology,2005,71(12):7799-7805.
[173] Eiler A, Bertilsson S. Composition of freshwater bacterial communities associated withcyanobacterial blooms in four Swedish lakes[J]. Environmental Microbiology,2004,6(12):1228-1243.
[174] Davidson K, Gilpin LC, Hart MC, et al. The influence of the balance of inorganic and organicnitrogen on the trophic dynamics of microbial food webs[J]. Limnology and Oceanography,2007,52(5):2147-2163.
[175] Allen AE, Booth MG, Verity PG, et al. Influence of nitrate availability on the distribution andabundance of heterotrophic bacterial nitrate assimilation genes in the Barents Sea duringsummer[J]. Aquatic Microbial Ecology,2005,39(3):247-255.
[176] Burr MD, Clark SJ, Spear CR, et al. Denaturing gradient gel electrophoresis can rapidlydisplay the bacterial diversity contained in16S rDNA clone libraries[J]. Microbial Ecology,2006,51(4):479-486.
[177] Logue JB, Burgmann H, Robinson CT. Progress in the ecological genetics and biodiversity offreshwater bacteria[J]. Bioscience,2008,58(2):103-113.
[178] Muyzer G. DGGE/TGGE a method for identifying genes from natural ecosystems[J]. CurrentOpinion in Microbiology,1999,2(3):317-322.
[179] Muyzer G, Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) andtemperature gradient gel electrophoresis (TGGE) in microbial ecology[J]. Antonie VanLeeuwenhoek International Journal of General and Molecular Microbiology,1998,73(1):127-141.
[180] Keohavong P, Thilly WG. Fidelity of DNApolymerases in DNAamplification[J]. Proceedingsof the National Academy of Sciences of the United States of America,1989,86(23):9253-9257.
[181] Sekiguchi H, Watanabe M, Nakahara T, et al. Succession of bacterial community structurealong the Changjiang River determined by denaturing gradient gel electrophoresis and clonelibrary analysis[J]. Applied and Environmental Microbiology,2002,68(10):5142-5150.
[182] Haack SK, Fogarty LR, West TG, et al. Spatial and temporal changes in microbial communitystructure associated with recharge-influenced chemical gradients in a contaminated aquifer[J].Environmental Microbiology,2004,6(5):438-448.
[183] Crump BC, Adams HE, Hobbie JE, et al. Biogeography of bacterioplankton in lakes andstreams of an arctic tundra catchment[J]. Ecology,2007,88(6):1365-1378.
[184] Lane DJ.16S/23S rRNA sequencing[M]//STACKEBRANDT E, GOODFELLOW M D.Nucleic Acid Techniques in Bacterial Systematic. New York; John Wiley and Sons.1991:115-175.
[185] Shannon AE, Weaver W. The mathematical theory of communication[M]. Urbana, IL:University Illinois Press,1963.
[186] Pielou EC. An Introduction to Mathematical Ecology[M]. New York: Wiley,1969.
[187] Clarke KR. Nonparametric multivariate analyses of changes in community structure[J].Australian Journal of Ecology,1993,18(1):117-143.
[188] Ehrich S, Behrens D, Lebedeva E, et al. A new obligately chemolithoautotrophic,nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogeneticrelationship[J]. Archives of Microbiology,1995,164(1):16-23.
[189] de Araujo JC, Schneider RP. DGGE with genomic DNA: suitable for detection of numericallyimportant organisms but not for identification of the most abundant organisms[J]. WaterResearch,2008,42(20):5002-5010.
[190] Diez B, Pedros-Alio C, Marsh TL, et al. Application of denaturing gradient gel electrophoresis(DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison ofDGGE with other molecular techniques[J]. Applied and Environmental Microbiology,2001,67(7):2942-2951.
[191] Kobayashi Y, Kim C, Yoshimizu C, et al. Longitudinal changes in bacterial communitycomposition in river epilithic biofilms: influence of nutrients and organic matter[J]. AquaticMicrobial Ecology,2009,54(2):135-152.
[192] Ogino A, Koshikawa H, Nakahara T, et al. Succession of microbial communities during abiostimulation process as evaluated by DGGE and clone library analyses[J]. Journal ofApplied Microbiology,2001,91(4):625-635.
[193] Sanz JL, Kochling T. Molecular biology techniques used in wastewater treatment: Anoverview[J]. Process Biochemistry,2007,42(2):119-133.
[194] Sekiguchi H, Tomioka N, Nakahara T, et al. A single band does not always represent singlebacterial strains in denaturing gradient gel electrophoresis analysis[J]. Biotechnology Letters,2001,23(15):1205-1208.
[195] Feng BW, Li XR, Wang JH, et al. Bacterial diversity of water and sediment in the Changjiangestuary and coastal area of the East China Sea[J]. FEMS Microbiology Ecology,2009,70(2):236-248.
[196] de Figueiredo DR, Pereira MJ, Moura A, et al. Bacterial community composition over a drywinter in meso-and eutrophic Portuguese water bodies[J]. FEMS Microbiology Ecology,2007,59(3):638-650.
[197] Tiquia SM, Schleibak M, Schlaff J, et al. Microbial community profiling and characterizationof some heterotrophic bacterial isolates from river waters and shallow groundwater wellsalong the rouge river, southeast Michigan[J]. Environmental Technology,2008,29(6):651-663.
[198] O'Sullivan LA, Weightman AJ, Fry JC. New degenerateCytophaga-Flexibacter-Bacteroides-specific16S ribosomal DNA-targeted oligonucleotideprobes reveal high bacterial diversity in River Taff epilithon[J]. Applied and EnvironmentalMicrobiology,2002,68(1):201-210.
[199] Feris KP, Ramsey PW, Frazar C, et al. Seasonal dynamics of shallow-hyporheic-zonemicrobial community structure along a heavy-metal contamination gradient[J]. Applied andEnvironmental Microbiology,2004,70(4):2323-2331.
[200] Leigh C, Burford MA, Roberts DT, et al. Predicting the vulnerability of reservoirs to poorwater quality and cyanobacterial blooms[J]. Water Research,2010,44(15):4487-4496.
[201] Rasche F, Knapp D, Kaiser C, et al. Seasonality and resource availability control bacterial andarchaeal communities in soils of a temperate beech forest[J]. ISME J,2011,5(3):389-402.
[202] Kowalchuk GA, Stephen JR. Ammonia-oxidizing bacteria: A model for molecular microbialecology[J]. Annual Review of Microbiology,2001,55:485-529.
[203] Winogradsky S. Recherches sur les organismes de la nitrification[J]. Computer Rendu,1890,110:1013-1016.
[204] Venter JC, Remington K, Heidelberg JF, et al. Environmental genome shotgun sequencing ofthe Sargasso Sea[J]. Science,2004,304(5667):66-74.
[205] Treusch AH, Leininger S, Kletzin A, et al. Novel genes for nitrite reductase and Amo-relatedproteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling[J].Environmental Microbiology,2005,7(12):1985-1995.
[206] Leininger S, Urich T, Schloter M, et al. Archaea predominate among ammonia-oxidizingprokaryotes in soils[J]. Nature,2006,442(7104):806-809.
[207] Onodera Y, Nakagawa T, Takahashi R, et al. Seasonal change in vertical distribution ofammonia-oxidizing archaea and bacteria and their nitrification in temperate forest soil[J].Microbes and Environments,2010,25(1):28-35.
[208] Adair KL, Schwartz E. Evidence that ammonia-oxidizing archaea are more abundant thanammonia-oxidizing bacteria in semiarid soils of northern Arizona, USA[J]. Microbial Ecology,2008,56(3):420-426.
[209] Chen XP, Zhu YG, Xia Y, et al. Ammonia-oxidizing archaea: important players in paddyrhizosphere soil?[J]. Environmental Microbiology,2008,10(8):1978-1987.
[210] Herrmann M, Saunders AM, Schramm A. Archaea dominate the ammonia-oxidizingcommunity in the rhizosphere of the freshwater macrophyte Littorella uniflora[J]. Applied andEnvironmental Microbiology,2008,74(10):3279-3283.
[211] Zhang LM, Wang M, Prosser JI, et al. Altitude ammonia-oxidizing bacteria and archaea insoils of Mount Everest[J]. FEMS Microbiology Ecology,2009,70(2):208-217.
[212] Wuchter C, Abbas B, Coolen MJL, et al. Archaeal nitrification in the ocean[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2006,103(33):12317-12322.
[213] Mincer TJ, Church MJ, Taylor LT, et al. Quantitative distribution of presumptive archaeal andbacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre[J]. EnvironmentalMicrobiology,2007,9(5):1162-1175.
[214] Beman JM, Popp BN, Francis CA. Molecular and biogeochemical evidence for ammoniaoxidation by marine Crenarchaeota in the Gulf of California[J]. Isme Journal,2008,2(4):429-441.
[215] Lam P, Jensen MM, Lavik G, et al. Linking crenarchaeal and bacterial nitrification toanammox in the Black Sea[J]. Proceedings of the National Academy of Sciences of the UnitedStates of America,2007,104(17):7104-7109.
[216] Nakagawa T, Mori K, Kato C, et al. Distribution of cold-adapted ammonia-oxidizingmicroorganisms in the deep-ocean of the northeastern Japan Sea[J]. Microbes andEnvironments,2007,22(4):365-372.
[217] Coolen MJL, Abbas B, van Bleijswijk J, et al. Putative ammonia-oxidizing Crenarchaeota insuboxic waters of the Black Sea: a basin-wide ecological study using16S ribosomal andfunctional genes and membrane lipids[J]. Environmental Microbiology,2007,9(4):1001-1016.
[218] Park SJ, Park BJ, Rhee SK. Comparative analysis of archaeal16S rRNA and amoA genes toestimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments[J].Extremophiles,2008,12(4):605-615.
[219] Kalanetra KM, Bano N, Hollibaugh JT. Ammonia-oxidizing Archaea in the Arctic Ocean andAntarctic coastal waters[J]. Environmental Microbiology,2009.
[220] Beman JM, Roberts KJ, Wegley L, et al. Distribution and diversity of archaeal ammoniamonooxygenase genes associated with corals[J]. Applied and Environmental Microbiology,2007,73(17):5642-5647.
[221] Steger D, Ettinger-Epstein P, Whalan S, et al. Diversity and mode of transmission ofammonia-oxidizing archaea in marine sponges[J]. Environmental Microbiology,2008,10(4):1087-1094.
[222] Beman JM, Francis CA. Diversity of ammonia-oxidizing archaea and bacteria in thesediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico[J]. Applied andEnvironmental Microbiology,2006,72(12):7767-7777.
[223] Caffrey JM, Bano N, Kalanetra K, et al. Ammonia oxidation and ammonia-oxidizing bacteriaand archaea from estuaries with differing histories of hypoxia[J]. Isme Journal,2007,1(7):660-662.
[224] Santoro AE, Francis CA, de Sieyes NR, et al. Shifts in the relative abundance ofammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterraneanestuary[J]. Environmental Microbiology,2008,10(4):1068-1079.
[225] Weidler GW, Dornmayr-Pfaffenhuemer M, Gerbl FW, et al. Communities of Archaea andBacteria in a subsurface radioactive thermal spring in the Austrian Central Alps, and evidenceof ammonia-oxidizing Crenarchaeota[J]. Applied and Environmental Microbiology,2007,73(1):259-270.
[226] Pouliot J, Galand PE, Lovejoy C, et al. Vertical structure of archaeal communities and thedistribution of ammonia monooxygenase A gene variants in two meromictic High Arcticlakes[J]. Environmental Microbiology,2009,11(3):687-699.
[227] van der Wielen P, Voost S, van der Kooij D. Ammonia-Oxidizing Bacteria and Archaea inGroundwater Treatment and Drinking Water Distribution Systems[J]. Applied andEnvironmental Microbiology,2009,75(14):4687-4695.
[228] Park HD, Wells GF, Bae H, et al. Occurrence of ammonia-oxidizing archaea in wastewatertreatment plant bioreactors[J]. Applied and Environmental Microbiology,2006,72(8):5643-5647.
[229] Zhang T, Jin T, Yan Q, et al. Occurrence of ammonia-oxidizing Archaea in activated sludgesof a laboratory scale reactor and two wastewater treatment plants[J]. Journal of AppliedMicrobiology,2009,107(3):970-977.
[230] Wells GF, Park HD, Yeung CH, et al. Ammonia-oxidizing communities in a highly aeratedfull-scale activated sludge bioreactor: betaproteobacterial dynamics and low relativeabundance of Crenarchaea[J]. Environmental Microbiology,2009,11(9):2310-2328.
[231] Schleper C, Jurgens G, Jonuscheit M. Genomic studies of uncultivated archaea[J]. NatureReviews Microbiology,2005,3(6):479-488.
[232] Konneke M, Bernhard AE, de la Torre JR, et al. Isolation of an autotrophicammonia-oxidizing marine archaeon[J]. Nature,2005,437(7058):543-546.
[233] de la Torre JR, Walker CB, Ingalls AE, et al. Cultivation of a thermophilic ammonia oxidizingarchaeon synthesizing crenarchaeol[J]. Environmental Microbiology,2008,10(3):810-818.
[234] Hatzenpichler R, Lebecleva EV, Spieck E, et al. A moderately thermophilicammonia-oxidizing crenarchaeote from a hot spring[J]. Proceedings of the National Academyof Sciences of the United States of America,2008,105(6):2134-2139.
[235] Tourna M, Stieglmeier M, Spang A, et al. Nitrososphaera viennensis, an ammonia oxidizingarchaeon from soil[J]. Proceedings of the National Academy of Sciences of the United Statesof America,2011,108(20):8420-8425.
[236] Nicol GW, Leininger S, Schleper C, et al. The influence of soil pH on the diversity, abundanceand transcriptional activity of ammonia oxidizing archaea and bacteria[J]. EnvironmentalMicrobiology,2008,10(11):2966-2978.
[237] Mosier AC, Francis CA. Relative abundance and diversity of ammonia-oxidizing archaea andbacteria in the San Francisco Bay estuary[J]. Environmental Microbiology,2008,10(11):3002-3016.
[238] Sahan E, Muyzer G. Diversity and spatio-temporal distribution of ammonia-oxidizing Archaeaand Bacteria in sediments of the Westerschelde estuary[J]. FEMS Microbiology Ecology,2008,64(2):175-186.
[239] Herrmann M, Saunders AM, Schramm A. Effect of lake trophic status and rooted macrophyteson community composition and abundance of ammonia-oxidizing prokaryotes in freshwatersediments[J]. Applied and Environmental Microbiology,2009,75(10):3127-3136.
[240] Ye W, Liu X, Lin S, et al. The vertical distribution of bacterial and archaeal communities inthe water and sediment of Lake Taihu[J]. FEMS Microbiology Ecology,2009,70(2):107-120.
[241] Lee JHW, Wang ZY, Thoe W, et al. Integrated physical and ecological management of the EastRiver[J]. Sustainable and Safe Water Supplies,2007,7(2):81-91.
[242] Francis CA, Roberts KJ, Beman JM, et al. Ubiquity and diversity of ammonia-oxidizingarchaea in water columns and sediments of the ocean[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2005,102(41):14683-14688.
[243] Rotthauwe JH, Witzel KP, Liesack W. The ammonia monooxygenase structural gene amoAasa functional marker: molecular fine-scale analysis of natural ammonia-oxidizingpopulations[J]. Applied and Environmental Microbiology,1997,63(12):4704-4712.
[244] Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool[J]. J Mol Biol,1990,215(3):403-410.
[245] Huber T, Faulkner G, Hugenholtz P. Bellerophon: a program to detect chimeric sequences inmultiple sequence alignments[J]. Bioinformatics,2004,20(14):2317-2319.
[246] Schloss PD, Handelsman J. Introducing DOTUR, a computer program for defining operationaltaxonomic units and estimating species richness[J]. Applied and Environmental Microbiology,2005,71(3):1501-1506.
[247] Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetictrees[J]. Mol Biol Evol,1987,4(4):406-425.
[248] Okano Y, Hristova KR, Leutenegger CM, et al. Application of real-time PCR to study effectsof ammonium on population size of ammonia-oxidizing bacteria in soil[J]. Applied andEnvironmental Microbiology,2004,70(2):1008-1016.
[249] Chain P, Lamerdin J, Larimer F, et al. Complete genome sequence of the ammonia-oxidizingbacterium and obligate chemolithoautotroph Nitrosomonas europaea[J]. Journal ofBacteriology2003,185(9):2759-2773.
[250] Smil V, Yushi M. The economic costs of China's environmental degradation[M]. Beijing,China: American Academy of Arts and Sciences,1998.
[251] Bollmann A, Bar-Gilissen MJ, Laanbroek HJ. Growth at low ammonium concentrations andstarvation response as potential factors involved in niche differentiation amongammonia-oxidizing bacteria[J]. Applied and Environmental Microbiology,2002,68(10):4751-4757.
[252] Koops HP, Pommerening-Roser A. Distribution and ecophysiology of the nitrifying bacteriaemphasizing cultured species[J]. FEMS Microbiology Ecology,2001,37(1):1-9.
[253] Schramm A, de Beer D, van den Heuvel JC, et al. Microscale distribution of populations andactivities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifyingbioreactor: Quantification by in situ hybridization and the use of microsensors[J]. Applied andEnvironmental Microbiology,1999,65(8):3690-3696.
[254] Cavicchioli R, DeMaere MZ, Thomas T. Metagenomic studies reveal the critical andwide-ranging ecological importance of uncultivated archaea: the role of ammonia oxidizers[J].Bioessays,2007,29(1):11-14.
[255] Zhang T, Jin T, Yan Q, et al. Occurrence of ammonia-oxidizing Archaea in activated sludgesof a laboratory scale reactor and two wastewater treatment plants[J]. Journal of AppliedMicrobiology,2009.
[256] Erguder TH, Boon N, Wittebolle L, et al. Environmental factors shaping the ecological nichesof ammonia-oxidizing archaea[J]. FEMS Microbiology Reviews2009,33(5):855-869.
[257] Jiang HC, Dong HL, Yu BS, et al. Diversity and abundance of ammonia-oxidizing archaea andbacteria in Qinghai Lake, northwestern China[J]. Geomicrobiology Journal,2009,26(3):199-211.
[258] Martens-Habbena W, Berube PM, Urakawa H, et al. Ammonia oxidation kinetics determineniche separation of nitrifying Archaea and Bacteria[J]. Nature,2009,461(7266):976-U234.
[259] Park BJ, Park SJ, Yoon DN, et al. Cultivation of autotrophic ammonia-oxidizing archaea frommarine sediments in co-culture with sulfur-oxidizing bacteria[J]. Applied and EnvironmentalMicrobiology,2010,76(22):7575-7587.
[260] Tourna M, Freitag TE, Nicol GW, et al. Growth, activity and temperature responses ofammonia-oxidizing archaea and bacteria in soil microcosms[J]. Environmental Microbiology,2008,10(5):1357-1364.
[261] Church MJ, Wai B, Karl DM, et al. Abundances of crenarchaeal amoAgenes and transcripts inthe Pacific Ocean[J]. Environmental Microbiology,2010,12(3):679-688.
[262] Di HJ, Cameron KC, Shen JP, et al. Nitrification driven by bacteria and not archaea innitrogen-rich grassland soils[J]. Nature Geoscience,2009,2(9):621-624.
[2] Karr JR, Chu EW. Sustaining living rivers[J]. Hydrobiologia,2000,422:1-14.
[3] Davis NM, Weaver V, Parks K, et al. An assessment of water quality, physical habitat, andbiological integrity of an urban stream in Wichita, Kansas, prior to restoration improvements(phase I)[J]. Archives of Environmental Contamination and Toxicology,2003,44(3):351-359.
[4] Magdaleno A, Puig A, de Cabo L, et al. Water pollution in an urban Argentine river[J].Bulletin of Environmental Contamination and Toxicology,2001,67(3):408-415.
[5]中华人民共和国水利部,《2008年中国水质量资源年报》,http://www.hydroinfo.gov.cn/gb/szyzlnb/.
[6]中华人民共和国环境保护部,2009年中国环境状况公报[R].北京.
[7]宋巍.东江流域农村饮用水源中微生物多样性研究及水质污染现状调查[D].陕西杨凌:西北农林科技大学,2009.
[8]金辉,张虎.东江干流水质变化趋势研究[J].上海环境科学,2000,19(z1):90-92.
[9] Galloway JN, Schlesinger WH, Levy H, et al. Nitrogen fixation: anthropogenicenhancement-environmental response[J]. Global Biogeochemical Cycles,1995,9(2):235-252.
[10] Galloway JN. The global nitrogen cycle: changes and consequences[J]. Environment Pollution,1998,102:15-24.
[11]胡国臣,张清敏.地下水硝酸盐氮污染防治研究[J].胡国臣,1999,18(5):228-230.
[12]张兴昌,邵明安.侵蚀条件下土壤氮素流失对土壤和环境的影响[J].土壤与环境,2000,9(3):249-252.
[13] Howarth RW, Billen G, Swaney D, et al. Regional nitrogen budgets and riverine N&P fluxesfor the drainages to the North Atlantic Ocean: natural and human influences[J].Biogeochemistry,1996,35(1):75-139.
[14] Turner RE, Rabalais NN. Changes in Mississippi River water-quality this century[J].Bioscience,1991,41(3):140-147.
[15] Justic D, Rabalais NN, Turner RE, et al. Changes in nutrient structure of river-dominatedcoastal waters-stoichiometric nutrient balance and Its consequences[J]. Estuarine CoastalAnd Shelf Science,1995,40(3):339-356.
[16] Vitousek PM, Aber JD, Howarth RW, et al. Human alteration of the global nitrogen cycle:sources and consequences[J]. Ecological Applications,1997,7(3):737-750.
[17] Peierls BL, Caraco NF, Pace ML, et al. Human influence on river nitrogen[J]. Nature,1991,350(6317):386-387.
[18]夏星辉,周劲松,杨志峰,等.黄河流域河水氮污染分析[J].环境科学学报,2001,21(5):563-568.
[19] Mulholland PJ, Helton AM, Poole GC, et al. Stream denitrification across biomes and itsresponse to anthropogenic nitrate loading[J]. Nature,2008,452(7184):202-205.
[20] Galloway JN, Townsend AR, Erisman JW, et al. Transformation of the nitrogen cycle: recenttrends, questions, and potential solutions[J]. Science,2008,320(5878):889-892.
[21] Gruber N, Galloway JN. An Earth-system perspective of the global nitrogen cycle[J]. Nature,2008,451(7176):293-296.
[22]叶辉,许建华.饮用水中的氨氮问题[J].中国给水排水,2000,(11):31-34.
[23]李玉婷.成都驷马桥水厂源水氨氮超标的处理工艺和运行[J].铁道劳动安全卫生与环保,2008,(01):21-23.
[24] Stigter TY, Ribeiro L, Dill AMMC. Application of a groundwater quality index as anassessment and communication tool in agro-environmental policies-Two Portuguese casestudies[J]. Journal of Hydrology,2006,327(3-4):578-591.
[25] Rabalais NN. Nitrogen in aquatic ecosystems[J]. Ambio,2002,31(2):102-112.
[26]毛战坡,单保庆,彭文启,等.氮素在河流生态系统中的滞留研究进展[J].长江流域资源与环境,2006,15(4):480-484.
[27] Zehr JP. Nitrogen fixation by marine cyanobacteria[J]. Trends in Microbiology,2011,19(4):162-173.
[28] K nneke M, Bernhard AE, de la Torre JR, et al. Isolation of an autotrophicammonia-oxidizing marine archaeon[J]. Nature,2005,437(7058):543-546.
[29] Nicol GW, Schleper C. Ammonia-oxidising Crenarchaeota: important players in the nitrogencycle?[J]. Trends in Microbiology,2006,14(5):207-212.
[30] Robertson LA, Kuenen JG. Aerobic denitrification: a controversy revived[J]. Archives ofMicrobiology,1984,139(4):351-354.
[31] Patureau D, Zumstein E, Delgenes JP, et al. Aerobic denitrifiers isolated from diverse naturaland managed ecosystems[J]. Microbial Ecology,2000,39(2):145-152.
[32] Lukow T, Diekmann H. Aerobic denitrification by a newly isolated heterotrophic bacteriumstrain TL1[J]. Biotechnology Letters,1997,19(11):1157-1159.
[33] Jorgensen KS, Tiedje JM. Survival of denitrifiers in nitrate-free, anaerobic environments[J].Applied and Environmental Microbiology,1993,59(10):3297-3305.
[34] Zumft WG. Cell biology and molecular basis of denitrification[J]. Microbiology andMolecular Biology Reviews,1997,61(4):533-616.
[35] Seitzinger S, Harrison JA, Bohlke JK, et al. Denitrification across landscapes and waterscapes:a synthesis[J]. Ecological Applications,2006,16(6):2064-2090.
[36] Richards FA. Anoxic basins and fjords[M]//RIPLEY J P, SKIRROW G A. ChemicalOceanography. London; Academic Press.1965:611-645.
[37] Mulder A, Vandegraaf AA, Robertson LA, et al. Anaerobic ammonium oxidation discoveredin a denitrifying fluidized bed reactor[J]. FEMS Microbiology Ecology,1995,16(3):177-183.
[38] Strous M, Fuerst JA, Kramer EHM, et al. Missing lithotroph identified as newplanctomycete[J]. Nature,1999,400(6743):446-449.
[39] van Niftrik LA, Fuerst JA, Damste JSS, et al. The anammoxosome: an intracytoplasmiccompartment in anammox bacteria[J]. FEMS Microbiology Letters,2004,233(1):7-13.
[40] Schubert CJ, Durisch-Kaiser E, Wehrli B, et al. Anaerobic ammonium oxidation in a tropicalfreshwater system (Lake Tanganyika)[J]. Environmental Microbiology,2006,8(10):1857-1863.
[41] Zhang Y, Ruan XH, den Camp HJMO, et al. Diversity and abundance of aerobic andanaerobic ammonium-oxidizing bacteria in freshwater sediments of the Xinyi River (China)[J].Environmental Microbiology,2007,9(9):2375-2382.
[42] Strous M, Pelletier E, Mangenot S, et al. Deciphering the evolution and metabolism of ananammox bacterium from a community genome[J]. Nature,2006,440(7085):790-794.
[43] Jetten MSM, van Niftrik L, Strous M, et al. Biochemistry and molecular biology of anammoxbacteria[J]. Critical Reviews in Biochemistry and Molecular Biology,2009,44(2-3):65-84.
[44] Cotner JB, Biddanda BA. Small players, large role: Microbial influence on biogeochemicalprocesses in pelagic aquatic ecosystems[J]. Ecosystems,2002,5(2):105-121.
[45] Arrigo KR. Marine microorganisms and global nutrient cycles[J]. Nature,2005,437(7057):349-355.
[46] Francis CA, Beman JM, Kuypers MMM. New processes and players in the nitrogen cycle: themicrobial ecology of anaerobic and archaeal ammonia oxidation[J]. Isme Journal,2007,1(1):19-27.
[47] Jetten MSM, Cirpus I, Kartal B, et al.1994-2004:10years of research on the anaerobicoxidation of ammonium[J]. Biochemical Society Transactions,2005,33:119-123.
[48] den Camp HJMO, Kartal B, Guven D, et al. Global impact and application of the anaerobicammonium-oxidizing (anammox) bacteria[J]. Biochemical Society Transactions,2006,34:174-178.
[49] Penton CR, Devol AH, Tiedje JM. Molecular evidence for the broad distribution of anaerobicammonium-oxidizing bacteria in freshwater and marine sediments[J]. Applied andEnvironmental Microbiology,2006,72(10):6829-6832.
[50] Kartal B, Kuypers MMM, Lavik G, et al. Anammox bacteria disguised as denitrifiers: nitratereduction to dinitrogen gas via nitrite and ammonium[J]. Environmental Microbiology,2007,9(3):635-642.
[51] Cabello P, Roldan MD, Moreno-Vivian C. Nitrate reduction and the nitrogen cycle inarchaea[J]. Microbiology-SGM,2004,150:3527-3546.
[52] Rittmann BE, Hausner M, Loffler F, et al. A vista for microbial ecology and environmentalbiotechnology[J]. Environmental Science&Technology,2006,40(4):1096-1103.
[53] Sharma R, Ranjan R, Kapardar RK, et al."Unculturable" bacterial diversity: an untappedresource[J]. Current Science,2005,89(1):72-77.
[54] Amann RI, Ludwig W, Schleifer KH. Phylogenetic Identification and in-Situ Detection ofIndividual Microbial Cells without Cultivation[J]. Microbiological Reviews,1995,59(1):143-169.
[55]洪义国,孙谧,张云波,等.16S rRNA在海洋微生物系统分子分类鉴定及分子检测中的应用[J].海洋水产研究,2002,(01):58-63.
[56] Amann RI, Ludwig W, Schleifer KH. Phylogenetic Identification and in-Situ Detection ofIndividual Microbial-Cells without Cultivation[J]. Microbiological Reviews,1995,59(1):143-169.
[57] Hahn D, Amann RI, Ludwig W, et al. Detection of micro-organisms in soil after insituhybridization with ribosomal RNA-targeted, fluorescently labeled oligonucleotides[J]. Journalof General Microbiology,1992,138:879-887.
[58] Moter A, Gobel UB. Fluorescence in situ hybridization (FISH) for direct visualization ofmicroorganisms[J]. Journal of Microbiological Methods,2000,41(2):85-112.
[59] Gulledge J, Ahmad A, Steudler PA, et al. Family-and genus-level16S rRNA-targetedoligonucleotide probes for ecological studies of methanotrophic bacteria[J]. Applied andEnvironmental Microbiology,2001,67(10):4726-4733.
[60] Felske A, Akkermans ADL. Prominent occurrence of ribosomes from an uncultured bacteriumof the Verrucomicrobiales cluster in grassland soils[J]. Letters in Applied Microbiology,1998,26(3):219-223.
[61] Schwieger F, Tebbe CC. A new approach to utilize PCR-single-strand-conformationpolymorphism for16s rRNA gene-based microbial community analysis[J]. Applied andEnvironmental Microbiology,1998,64(12):4870-4876.
[62] Schwieger F, Tebbe CC. Effect of field inoculation with Sinorhizobium meliloti L33on thecomposition of bacterial communities in rhizospheres of a target plant (Medicago sativa) and anon-target plant (Chenopodium album)-Linking of16S rRNA gene-based single-strandconformation polymorphism community profiles to the diversity of cultivated bacteria[J].Applied and Environmental Microbiology,2000,66(8):3556-3565.
[63] Peters S, Koschinsky S, Schwieger F, et al. Succession of microbial communities during hotcomposting as detected by PCR-single-strand-conformation polymorphism-based geneticprofiles of small-subunit rRNA genes[J]. Applied and Environmental Microbiology,2000,66(3):930-936.
[64] Tiquia SM, Ichida JM, Keener HM, et al. Bacterial community profiles on feathers duringcomposting as determined by terminal restriction fragment length polymorphism analysis of16S rDNAgenes[J].Applied Microbiology and Biotechnology,2005,67(3):412-419.
[65] Smit E, Leeflang P, Wernars K. Detection of shifts in microbial community structure anddiversity in soil caused by copper contamination using amplified ribosomal DNA restrictionanalysis[J]. FEMS Microbiology Ecology,1997,23(3):249-261.
[66] Heyndrickx M, Vauterin L, Vandamme P, et al. Applicability of combined amplified ribosomalDNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy[J]. Journalof Microbiological Methods,1996,26(3):247-259.
[67] Sette LD, Simioni KCM, Vasconcellos SP, et al. Analysis of the composition of bacterialcommunities in oil reservoirs from a southern offshore Brazilian basin[J]. Antonie VanLeeuwenhoek International Journal of General and Molecular Microbiology,2007,91(3):253-266.
[68] Osborn AM, Moore ERB, Timmis KN. An evaluation of terminal-restriction fragment lengthpolymorphism (T-RFLP) analysis for the study of microbial community structure anddynamics[J]. Environmental Microbiology,2000,2(1):39-50.
[69] Dunbar J, Ticknor LO, Kuske CR. Phylogenetic specificity and reproducibility and newmethod for analysis of terminal restriction fragment profiles of16S rRNA genes frombacterial communities[J]. Applied and Environmental Microbiology,2001,67(1):190-197.
[70] Lukow T, Dunfield PF, Liesack W. Use of the T-RFLP technique to assess spatial and temporalchanges in the bacterial community structure within an agricultural soil planted withtransgenic and non-transgenic potato plants[J]. FEMS Microbiology Ecology,2000,32(3):241-247.
[71] Myers RM, Maniatis T, Lerman LS. Detection and localization of single base changes bydenaturing gradient gel electrophoresis[J]. Methods Enzymol,1987,155:501-527.
[72] Muyzer G, Dewaal EC, Uitterlinden AG. Profiling of complex microbial populations bydenaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genescoding for16S rRNA[J]. Applied and Environmental Microbiology,1993,59(3):695-700.
[73] Simpson JM, McCracken VJ, Gaskins HR, et al. Denaturing gradient gel electrophoresisanalysis of16S ribosomal DNAamplicons to monitor changes in fecal bacterial populations ofweaning pigs after introduction of Lactobacillus reuteri strain MM53[J]. Applied andEnvironmental Microbiology,2000,66(11):4705-4714.
[74] ben Omar N, Ampe F. Microbial community dynamics during production of the Mexicanfermented maize dough pozol[J]. Applied and Environmental Microbiology,2000,66(9):3664-3673.
[75] Cocolin L, Manzano M, Cantoni C, et al. Denaturing gradient gel electrophoresis analysis ofthe16S rRNA gene V1region to monitor dynamic changes in the bacterial population duringfermentation of Italian sausages[J]. Applied and Environmental Microbiology,2001,67(11):5113-5121.
[76] Takai K, Horikoshi K. Rapid detection and quantification of members of the archaealcommunity by quantitative PCR using fluorogenic probes[J]. Applied and EnvironmentalMicrobiology,2000,66(11):5066-5072.
[77] Ochsenreiter T, Selezi D, Quaiser A, et al. Diversity and abundance of Crenarchaeota interrestrial habitats studied by16S RNA surveys and real time PCR[J]. EnvironmentalMicrobiology,2003,5(9):787-797.
[78] James FC, Mcculloch CE. Multivariate analysis in ecology and systematics: panacea orpandora box?[J]. Annual Review of Ecology and Systematics1990,21:129-166.
[79] Franklin RB, Mills AL. Multi-scale variation in spatial heterogeneity for microbial communitystructure in an eastern Virginia agricultural field[J]. FEMS Microbiology Ecology,2003,44(3):335-346.
[80] Mouser PJ, Rizzo DM, Roling WF, et al. A multivariate statistical approach to spatialrepresentation of groundwater contamination using hydrochemistry and microbial communityprofiles[J]. Environmental Science&Technology,2005,39(19):7551-7559.
[81] Terbraak CJF. Canonical correspondence analysis: a new eigenvector technique formultivariate direct gradient analysis[J]. Ecology,1986,67(5):1167-1179.
[82] Ludvigsen L, Albrechtsen HJ, Holst H, et al. Correlating phospholipid fatty acids (PLFA) in alandfill leachate polluted aquifer with biogeochemical factors by multivariate statisticalmethods[J]. FEMS Microbiology Reviews1997,20(3-4):447-460.
[83] Weckstrom J, Korhola A. Patterns in the distribution, composition and diversity of diatomassemblages in relation to ecoclimatic factors in Arctic Lapland[J]. Journal of Biogeography,2001,28(1):31-45.
[84] Boon N, De Windt W, Verstraete W, et al. Evaluation of nested PCR-DGGE (denaturinggradient gel electrophoresis) with group-specific16S rRNA primers for the analysis ofbacterial communities from different wastewater treatment plants[J]. FEMS MicrobiologyEcology,2002,39(2):101-112.
[85] Stepanauskas R, Moran MA, Bergamaschi BA, et al. Covariance of bacterioplanktoncomposition and environmental variables in a temperate delta system[J]. Aquatic MicrobialEcology,2003,31(1):85-98.
[86] Cordova-Kreylos AL, Cao YP, Green PG, et al. Diversity, composition, and geographicaldistribution of microbial communities in california salt marsh Sediments[J]. Applied andEnvironmental Microbiology,2006,72(5):3357-3366.
[87] Ikenaga M, Guevara R, Dean AL, et al. Changes in community structure of sediment bacteriaalong the Florida Coastal Everglades marsh-mangrove-seagrass salinity gradient[J]. MicrobialEcology,2010,59(2):284-295.
[88]周红,张志南.大型多元统计软件PRIMER的方法原理及其在底栖群落生态学中的应用[J].青岛海洋大学学报(自然科学版),2003,(01):58-64.
[89] Ongley E. Modernization of water quality programs in developing countries: issues ofrelevancy and cost efficiency[J]. Water Quality International,1998:37-42.
[90] Debels P, Figueroa R, Urrutia R, et al. Evaluation of water quality in the Chillan River(Central Chile) using physicochemical parameters and a modified Water Quality Index[J].Environmental Monitoring andAssessment,2005,110(1-3):301-322.
[91] Rauch W, Henze M, Koncsos L, et al. River water quality modelling: I. State of the art[J].Water Science and Technology,1998,38(11):237-244.
[92] Shanahan P, Henze M, Koncsos L, et al. River water quality modelling: II. Problems of theart[J]. Water Science and Technology,1998,38(11):245-252.
[93] Somlyody L, Henze M, Koncsos L, et al. River water quality modelling: III. Future of theart[J]. Water Science and Technology,1998,38(11):253-260.
[94] Sanchez E, Colmenarejo MF, Vicente J, et al. Use of the water quality index and dissolvedoxygen deficit as simple indicators of watersheds pollution[J]. Ecological Indicators,2007,7(2):315-328.
[95] Kannel PR, Lee S, Lee YS, et al. Application of water quality indices and dissolved oxygen asindicators for river water classification and urban impact assessment[J]. EnvironmentalMonitoring andAssessment,2007,132(1-3):93-110.
[96] Cude CG. Oregon water quality index: A tool for evaluating water quality managementeffectiveness[J]. Journal of the American Water Resources Association,2001,37(1):125-137.
[97] Liou S-M, Lo S-L, Wang S-H. Ageneralized water quality index for Taiwan[J]. EnvironmentalMonitoring andAssessment,2004,96(1):35-52.
[98] Banerjee T, Srivastava RK. Application of water quality index for assessment of surface waterquality surrounding integrated industrial estate-Pantnagar[J]. Water Science and Technology,2009,60(8):2041-2053.
[99] Chaturvedi MK, Bassin JK. Assessing the water quality index of water treatment plant andbore wells, in Delhi, India[J]. Environmental Monitoring and Assessment,2010,163(1-4):449-453.
[100] Hills P, Zhang L, Liu J. Transboundary pollution between Guangdong Province and HongKong: threats to water quality in the Pearl River Estuary and their implications forenvironmental policy and planning[J]. Journal of Environmental Planning and Management,1998,41(3):375-396.
[101] Ho KC, Hui KC. Chemical contamination of the East River (Dongjiang) and its implication onsustainable development in the Pearl River Delta[J]. Environment International,2001,26(5-6):303-308.
[102] Shuhaimi-Othman M, Lim EC, Mushrifah I. Water quality changes in Chini Lake, Pahang,West Malaysia[J]. Environmental Monitoring andAssessment,2007,131(1-3):279-292.
[103] Bellos D, Sawidis T. Chemical pollution monitoring of the River Pinios (Thessalia-Greece)[J].Journal of Environmental Management,2005,76(4):282-292.
[104]陈静生,高学民,夏星辉,等.长江水系河水氮污染[J].环境化学,1999,(04):289-293.
[105]刘国华,傅伯杰,杨平.海河水环境质量及污染物入海通量[J].环境科学,2001,(04):46-50.
[106]毛剑英,朱建平,肖建军.近年来淮河干流氮污染状况与变化趋势[J].中国环境监测,2003,19(05):41-43.
[107]刘元波,高锡芸.太湖北部梅梁湾水域水质因子聚类[J].湖泊科学,1997,9(03):255-260.
[108]朱余,王凤.巢湖流域水质状况与环境目标可达性分析[J].环境监测管理与技术,2004,16(06):22-23,26.
[109]杨文龙，杨树华.滇池流域非点源污染控制区划研究[J].云南环境科学,1996,(03).
[110] Vega M, Pardo R, Barrado E, et al. Assessment of seasonal and polluting effects on the qualityof river water by exploratory data analysis[J]. Water Research,1998,32(12):3581-3592.
[111] Winter C, Hein T, Kavka G, et al. Longitudinal changes in the bacterial communitycomposition of the Danube River: a whole-river approach[J]. Applied and EnvironmentalMicrobiology,2007,73(2):421-431.
[112] Kirchman DL, Dittel AI, Findlay SEG, et al. Changes in bacterial activity and communitystructure in response to dissolved organic matter in the Hudson River, New York[J]. AquaticMicrobial Ecology,2004,35(3):243-257.
[113] Cebron A, Berthe T, Garnier J. Nitrification and nitrifying bacteria in the lower Seine Riverand estuary (France)[J]. Applied and Environmental Microbiology,2003,69(12):7091-7100.
[114] Cebron A, Coci M, Garnier J, et al. Denaturing gradient gel electrophoretic analysis ofammonia-oxidizing bacterial community structure in the lower Seine River: impact of Pariswastewater effluents[J]. Applied and Environmental Microbiology,2004,70(11):6726-6737.
[115] Crump BC, Armbrust EV, Baross JA. Phylogenetic analysis of particle-attached andfree-living bacterial communities in the Columbia river, its estuary, and the adjacent coastalocean[J]. Applied and Environmental Microbiology,1999,65(7):3192-3204.
[116] Stevens H, Ulloa O. Bacterial diversity in the oxygen minimum zone of the eastern tropicalSouth Pacific[J]. Environmental Microbiology,2008,10(5):1244-1259.
[117] Giovannoni SJ, Britschgi TB, Moyer CL, et al. Genetic diversity in Sargasso Seabacterioplankton[J]. Nature,1990,345(6270):60-63.
[118] Fuhrman JA, Mccallum K, Davis AA. Novel major archaebacterial group from marineplankton[J]. Nature,1992,356(6365):148-149.
[119] Sekiguchi H, Koshikawa H, Hiroki M, et al. Bacterial distribution and phylogenetic diversityin the Changjiang estuary before the construction of the Three Gorges Dam[J]. MicrobialEcology,2002,43(1):82-91.
[120] Hewson I, Fuhrman JA. Richness and diversity of bacterioplankton species along an estuarinegradient in Moreton Bay, Australia[J]. Applied and Environmental Microbiology,2004,70(6):3425-3433.
[121] Stehr G, Bottcher B, Dittberner P, et al. The ammonia-oxidizing nitrifying population of theRiver Elbe estuary[J]. FEMS Microbiology Ecology,1995,17(3):177-186.
[122] Ovreas L, Forney L, Daae FL, et al. Distribution of bacterioplankton in meromictic LakeSaelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplifiedgene fragments coding for16S rRNA[J]. Applied and Environmental Microbiology,1997,63(9):3367-3373.
[123] Li SK, Xiao X, Yin XB, et al. Bacterial community along a historic lake sediment core ofArdley Island, west Antarctica[J]. Extremophiles,2006,10(5):461-467.
[124] Gaidos E, Lanoil B, Thorsteinsson T, et al. A viable microbial community in a subglacialvolcanic crater lake, Iceland[J]. Astrobiology,2004,4(3):327-344.
[125] Zwart G, Crump BC, Agterveld MPKV, et al. Typical freshwater bacteria: an analysis ofavailable16S rRNA gene sequences from plankton of lakes and rivers[J]. Aquatic MicrobialEcology,2002,28(2):141-155.
[126] B ckelmann U, Manz W, Neu TR, et al. Characterization of the microbial community of loticorganic aggregates ('river snow') in the Elbe River of Germany by cultivation and molecularmethods[J]. FEMS Microbiology Ecology,2000,33(2):157-170.
[127] Li D, Yang M, Li Z, et al. Change of bacterial communities in sediments along Songhua Riverin Northeastern China after a nitrobenzene pollution event[J]. FEMS Microbiology Ecology,2008,65(3):494-503.
[128] Battin TJ, Wille A, Sattler B, et al. Phylogenetic and functional heterogeneity of sedimentbiofilms along environmental gradients in a glacial stream[J]. Applied and EnvironmentalMicrobiology,2001,67(2):799-807.
[129] Lemke MJ, Lienau EK, Rothe J, et al. Description of freshwater bacterial assemblages fromthe upper Parana River floodpulse system, Brazil[J]. Microbial Ecology,2009,57(1):94-103.
[130] Crump BC, Peterson BJ, Raymond PA, et al. Circumpolar synchrony in big riverbacterioplankton[J]. Proceedings of the National Academy of Sciences of the United States ofAmerica,2009,106(50):21208-21212.
[131] Herfort L, Schouten S, Abbas B, et al. Variations in spatial and temporal distribution ofArchaea in the North Sea in relation to environmental variables[J]. FEMS MicrobiologyEcology,2007,62(3):242-257.
[132] Goh F, Allen MA, Leuko S, et al. Determining the specific microbial populations and theirspatial distribution within the stromatolite ecosystem of Shark Bay[J]. Isme Journal,2009,3(4):383-396.
[133] Newton RJ, Jones SE, Eiler A, et al. A guide to the natural history of freshwater lakebacteria[J]. Microbiology and Molecular Biology Reviews,2011,75(1):14-49.
[134] Crump BC, Hobbie JE. Synchrony and seasonality in bacterioplankton communities of twotemperate rivers[J]. Limnology and Oceanography,2005,50(6):1718-1729.
[135] Zehr JP, Ward BB. Nitrogen cycling in the ocean: new perspectives on processes andparadigms[J]. Applied and Environmental Microbiology,2002,68(3):1015-1024.
[136] Mason OU, Di Meo-Savoie CA, Van Nostrand JD, et al. Prokaryotic diversity, distribution,and insights into their role in biogeochemical cycling in marine basalts[J]. Isme Journal,2009,3(2):231-242.
[137]金辉.东江干流东莞段水质研究[J].环境科学研究,2001,14(3):45-48.
[138]金辉,李榴芬,朱建民.东江中游水污染状况及其变化趋势[J].广西师院学报(自然科学版),2001,18(2):60-62.
[139] Liang Y, Fung PK, Tse MF, et al. Sources and seasonal variation of PAHs in the sediments ofdrinking water reservoirs in Hong Kong and the Dongjiang River (China)[J]. Environ MonitAssess,2008,146(1-3):41-50.
[140] Delong EF, Wickham GS, Pace NR. Phylogenetic stains: ribosomal RNA-based probes for theidentification of single cells[J]. Science,1989,243(4896):1360-1363.
[141] Gurtler V, Stanisich VA. New approaches to typing and identification of bacteria using the16S-23S rDNAspacer region[J]. Microbiology,1996,142:3-16.
[142] Hall T. Biological sequence alignment editor for Win95/98/NT/2K/XP.[M]. Carlsbad, CA: IbisBiosicences,1999.
[143] Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool[J]. Journal ofMolecular Biology1990,215(3):403-410.
[144] Cole JR, Wang Q, Cardenas E, et al. The Ribosomal Database Project: improved alignmentsand new tools for rRNAanalysis[J]. Nucleic Acids Research,2009,37: D141-145.
[145] Tamura K, Dudley J, Nei M, et al. MEGA4: molecular evolutionary genetics analysis (MEGA)software version4.0[J]. Molecular Biology and Evolution,2007,24(8):1596-1599.
[146] Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetictrees[J]. Molecular Biology and Evolution,1987,4(4):406-425.
[147] Kimura M. A simple method for estimating evolutionary rates of base substitutions throughcomparative studies of nucleotide sequences[J]. J Mol Evol,1980,16(2):111-120.
[148] Chao A, Bunge J. Estimating the number of species in a Stochastic abundance model[J].Biometrics,2002,58(3):531-539.
[149] Xu M, Wu WM, Wu L, et al. Responses of microbial community functional structures topilot-scale uranium in situ bioremediation[J]. ISME J,2010,4:1060-1070.
[150] ter Braak CJF, milauer P. CANOCO reference manual and CanoDraw for Windows user'sguide: software for canonical community ordination (version4.5).[M]. Ithaca NY, USA;Microcomputer Power.2002:500.
[151] Schloss PD, Larget BR, Handelsman J. Integration of microbial ecology and statistics: a test tocompare gene libraries[J]. Applied and Environmental Microbiology,2004,70(9):5485-5492.
[152] Hahn MW, Kasalicky V, Jezbera J, et al. Limnohabitans curvus gen. nov., sp nov., a planktonicbacterium isolated from a freshwater lake[J]. International Journal of Systematic andEvolutionary Microbiology,2010,60:1358-1365.
[153] Heckmann K, Schmidt HJ. Polynucleobacter necessarius gen. nov., sp. nov., an obligatelyendosymbiotic bacterium living in the cytoplasm of Euplotes aediculatus[J]. InternationalJournal of Systematic Bacteriology,1987,37(4):456-457.
[154] Jezbera J, Jezberova J, Brandt U, et al. Ubiquity of Polynucleobacter necessarius subspeciesasymbioticus results from ecological diversification[J]. Environmental Microbiology,2011,13(4):922-931.
[155] Hiorns WD, Methe BA, NierzwickiBauer SA, et al. Bacterial diversity in AdirondackMountain lakes as revealed by16S rRNA gene sequences[J]. Applied and EnvironmentalMicrobiology,1997,63(7):2957-2960.
[156] Zwart G, Hiorns WD, Methe BA, et al. Nearly identical16S rRNA sequences recovered fromlakes in North America and Europe indicate the existence of clades of globally distributedfreshwater bacteria[J]. Systematic andApplied Microbiology,1998,21(4):546-556.
[157] Wu X, Xi WY, Ye WJ, et al. Bacterial community composition of a shallow hypertrophicfreshwater lake in China, revealed by16S rRNA gene sequences[J]. FEMS MicrobiologyEcology,2007,61(1):85-96.
[158] Newton RJ, Kent AD, Triplett EW, et al. Microbial community dynamics in a humic lake:differential persistence of common freshwater phylotypes[J]. Environmental Microbiology,2006,8(6):956-970.
[159] Simek K, Armengol J, Comerma M, et al. Changes in the epilimnetic bacterial communitycomposition, production, and protist-induced mortality along the longitudinal axis of a highlyeutrophic reservoir[J]. Microbial Ecology,2001,42(3):359-371.
[160] Simek K, Hornak K, Jezbera J, et al. Influence of top-down and bottom-up manipulations onthe R-BT065subcluster of beta-proteobacteria, an abundant group in bacterioplankton of afreshwater reservoir[J]. Applied and Environmental Microbiology,2005,71(5):2381-2390.
[161] Glockner FO, Zaichikov E, Belkova N, et al. Comparative16S rRNA analysis of lakebacterioplankton reveals globally distributed phylogenetic clusters including an abundantgroup of actinobacteria[J]. Applied and Environmental Microbiology,2000,66(11):5053-5065.
[162] Burkert U, Warnecke F, Babenzien D, et al. Members of a readily enrichedbeta-proteobacterial clade are common in surface waters of a humic lake[J]. Applied andEnvironmental Microbiology,2003,69(11):6550-6559.
[163] Hahn MW. Isolation of strains belonging to the cosmopolitan Polynucleobacter necessariuscluster from freshwater habitats located in three climatic zones[J]. Applied and EnvironmentalMicrobiology,2003,69(9):5248-5254.
[164] Head IM, Hiorns WD, Embley TM, et al. The phylogeny of autotrophic ammonia-oxidizingbacteria as determined by analysis of16s ribosomal-RNA rene-sequences[J]. Journal ofGeneral Microbiology,1993,139:1147-1153.
[165] Teske A, Hinrichs KU, Edgcomb V, et al. Microbial diversity of hydrothermal sediments in theGuaymas Basin: evidence for anaerobic methanotrophic communities[J]. Applied andEnvironmental Microbiology,2002,68(4):1994-2007.
[166] Maksimenko SY, Zemskaya TI, Pavlova ON, et al. Microbial community of the water columnof the Selenga River-Lake Baikal biogeochemical barrier[J]. Microbiology,2008,77(5):587-594.
[167] Xie CH, Yokota A. Sphingomonas azotifigens sp nov., a nitrogen-fixing bacterium isolatedfrom the roots of Oryza sativa[J]. International Journal of Systematic and EvolutionaryMicrobiology,2006,56:889-893.
[168] Warnecke F, Amann R, Pernthaler J. Actinobacterial16S rRNAgenes from freshwater habitatscluster in four distinct lineages[J]. Environmental Microbiology,2004,6(3):242-253.
[169] Sekar R, Pernthaler A, Pernthaler J, et al. An improved protocol for quantification offreshwater Actinobacteria by fluorescence in situ hybridization[J]. Applied and EnvironmentalMicrobiology,2003,69(5):2928-2935.
[170] Witzel KP, Overbeck HJ. Heterotrophic nitrification by Arthrobacter sp.(Strain9006) asinfluenced by different cultural conditions, growth state and acetate metabolism[J]. Archivesof Microbiology,1979,122(2):137-143.
[171] Brierley EDR, Wood M. Heterotrophic nitrification in an acid forest soil: isolation andcharacterisation of a nitrifying bacterium[J]. Soil Biology&Biochemistry,2001,33(10):1403-1409.
[172] Elifantz H, Malmstrom RR, Cottrell MT, et al. Assimilation of polysaccharides and glucose bymajor bacterial groups in the Delaware Estuary[J]. Applied and Environmental Microbiology,2005,71(12):7799-7805.
[173] Eiler A, Bertilsson S. Composition of freshwater bacterial communities associated withcyanobacterial blooms in four Swedish lakes[J]. Environmental Microbiology,2004,6(12):1228-1243.
[174] Davidson K, Gilpin LC, Hart MC, et al. The influence of the balance of inorganic and organicnitrogen on the trophic dynamics of microbial food webs[J]. Limnology and Oceanography,2007,52(5):2147-2163.
[175] Allen AE, Booth MG, Verity PG, et al. Influence of nitrate availability on the distribution andabundance of heterotrophic bacterial nitrate assimilation genes in the Barents Sea duringsummer[J]. Aquatic Microbial Ecology,2005,39(3):247-255.
[176] Burr MD, Clark SJ, Spear CR, et al. Denaturing gradient gel electrophoresis can rapidlydisplay the bacterial diversity contained in16S rDNA clone libraries[J]. Microbial Ecology,2006,51(4):479-486.
[177] Logue JB, Burgmann H, Robinson CT. Progress in the ecological genetics and biodiversity offreshwater bacteria[J]. Bioscience,2008,58(2):103-113.
[178] Muyzer G. DGGE/TGGE a method for identifying genes from natural ecosystems[J]. CurrentOpinion in Microbiology,1999,2(3):317-322.
[179] Muyzer G, Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) andtemperature gradient gel electrophoresis (TGGE) in microbial ecology[J]. Antonie VanLeeuwenhoek International Journal of General and Molecular Microbiology,1998,73(1):127-141.
[180] Keohavong P, Thilly WG. Fidelity of DNApolymerases in DNAamplification[J]. Proceedingsof the National Academy of Sciences of the United States of America,1989,86(23):9253-9257.
[181] Sekiguchi H, Watanabe M, Nakahara T, et al. Succession of bacterial community structurealong the Changjiang River determined by denaturing gradient gel electrophoresis and clonelibrary analysis[J]. Applied and Environmental Microbiology,2002,68(10):5142-5150.
[182] Haack SK, Fogarty LR, West TG, et al. Spatial and temporal changes in microbial communitystructure associated with recharge-influenced chemical gradients in a contaminated aquifer[J].Environmental Microbiology,2004,6(5):438-448.
[183] Crump BC, Adams HE, Hobbie JE, et al. Biogeography of bacterioplankton in lakes andstreams of an arctic tundra catchment[J]. Ecology,2007,88(6):1365-1378.
[184] Lane DJ.16S/23S rRNA sequencing[M]//STACKEBRANDT E, GOODFELLOW M D.Nucleic Acid Techniques in Bacterial Systematic. New York; John Wiley and Sons.1991:115-175.
[185] Shannon AE, Weaver W. The mathematical theory of communication[M]. Urbana, IL:University Illinois Press,1963.
[186] Pielou EC. An Introduction to Mathematical Ecology[M]. New York: Wiley,1969.
[187] Clarke KR. Nonparametric multivariate analyses of changes in community structure[J].Australian Journal of Ecology,1993,18(1):117-143.
[188] Ehrich S, Behrens D, Lebedeva E, et al. A new obligately chemolithoautotrophic,nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogeneticrelationship[J]. Archives of Microbiology,1995,164(1):16-23.
[189] de Araujo JC, Schneider RP. DGGE with genomic DNA: suitable for detection of numericallyimportant organisms but not for identification of the most abundant organisms[J]. WaterResearch,2008,42(20):5002-5010.
[190] Diez B, Pedros-Alio C, Marsh TL, et al. Application of denaturing gradient gel electrophoresis(DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison ofDGGE with other molecular techniques[J]. Applied and Environmental Microbiology,2001,67(7):2942-2951.
[191] Kobayashi Y, Kim C, Yoshimizu C, et al. Longitudinal changes in bacterial communitycomposition in river epilithic biofilms: influence of nutrients and organic matter[J]. AquaticMicrobial Ecology,2009,54(2):135-152.
[192] Ogino A, Koshikawa H, Nakahara T, et al. Succession of microbial communities during abiostimulation process as evaluated by DGGE and clone library analyses[J]. Journal ofApplied Microbiology,2001,91(4):625-635.
[193] Sanz JL, Kochling T. Molecular biology techniques used in wastewater treatment: Anoverview[J]. Process Biochemistry,2007,42(2):119-133.
[194] Sekiguchi H, Tomioka N, Nakahara T, et al. A single band does not always represent singlebacterial strains in denaturing gradient gel electrophoresis analysis[J]. Biotechnology Letters,2001,23(15):1205-1208.
[195] Feng BW, Li XR, Wang JH, et al. Bacterial diversity of water and sediment in the Changjiangestuary and coastal area of the East China Sea[J]. FEMS Microbiology Ecology,2009,70(2):236-248.
[196] de Figueiredo DR, Pereira MJ, Moura A, et al. Bacterial community composition over a drywinter in meso-and eutrophic Portuguese water bodies[J]. FEMS Microbiology Ecology,2007,59(3):638-650.
[197] Tiquia SM, Schleibak M, Schlaff J, et al. Microbial community profiling and characterizationof some heterotrophic bacterial isolates from river waters and shallow groundwater wellsalong the rouge river, southeast Michigan[J]. Environmental Technology,2008,29(6):651-663.
[198] O'Sullivan LA, Weightman AJ, Fry JC. New degenerateCytophaga-Flexibacter-Bacteroides-specific16S ribosomal DNA-targeted oligonucleotideprobes reveal high bacterial diversity in River Taff epilithon[J]. Applied and EnvironmentalMicrobiology,2002,68(1):201-210.
[199] Feris KP, Ramsey PW, Frazar C, et al. Seasonal dynamics of shallow-hyporheic-zonemicrobial community structure along a heavy-metal contamination gradient[J]. Applied andEnvironmental Microbiology,2004,70(4):2323-2331.
[200] Leigh C, Burford MA, Roberts DT, et al. Predicting the vulnerability of reservoirs to poorwater quality and cyanobacterial blooms[J]. Water Research,2010,44(15):4487-4496.
[201] Rasche F, Knapp D, Kaiser C, et al. Seasonality and resource availability control bacterial andarchaeal communities in soils of a temperate beech forest[J]. ISME J,2011,5(3):389-402.
[202] Kowalchuk GA, Stephen JR. Ammonia-oxidizing bacteria: A model for molecular microbialecology[J]. Annual Review of Microbiology,2001,55:485-529.
[203] Winogradsky S. Recherches sur les organismes de la nitrification[J]. Computer Rendu,1890,110:1013-1016.
[204] Venter JC, Remington K, Heidelberg JF, et al. Environmental genome shotgun sequencing ofthe Sargasso Sea[J]. Science,2004,304(5667):66-74.
[205] Treusch AH, Leininger S, Kletzin A, et al. Novel genes for nitrite reductase and Amo-relatedproteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling[J].Environmental Microbiology,2005,7(12):1985-1995.
[206] Leininger S, Urich T, Schloter M, et al. Archaea predominate among ammonia-oxidizingprokaryotes in soils[J]. Nature,2006,442(7104):806-809.
[207] Onodera Y, Nakagawa T, Takahashi R, et al. Seasonal change in vertical distribution ofammonia-oxidizing archaea and bacteria and their nitrification in temperate forest soil[J].Microbes and Environments,2010,25(1):28-35.
[208] Adair KL, Schwartz E. Evidence that ammonia-oxidizing archaea are more abundant thanammonia-oxidizing bacteria in semiarid soils of northern Arizona, USA[J]. Microbial Ecology,2008,56(3):420-426.
[209] Chen XP, Zhu YG, Xia Y, et al. Ammonia-oxidizing archaea: important players in paddyrhizosphere soil?[J]. Environmental Microbiology,2008,10(8):1978-1987.
[210] Herrmann M, Saunders AM, Schramm A. Archaea dominate the ammonia-oxidizingcommunity in the rhizosphere of the freshwater macrophyte Littorella uniflora[J]. Applied andEnvironmental Microbiology,2008,74(10):3279-3283.
[211] Zhang LM, Wang M, Prosser JI, et al. Altitude ammonia-oxidizing bacteria and archaea insoils of Mount Everest[J]. FEMS Microbiology Ecology,2009,70(2):208-217.
[212] Wuchter C, Abbas B, Coolen MJL, et al. Archaeal nitrification in the ocean[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2006,103(33):12317-12322.
[213] Mincer TJ, Church MJ, Taylor LT, et al. Quantitative distribution of presumptive archaeal andbacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre[J]. EnvironmentalMicrobiology,2007,9(5):1162-1175.
[214] Beman JM, Popp BN, Francis CA. Molecular and biogeochemical evidence for ammoniaoxidation by marine Crenarchaeota in the Gulf of California[J]. Isme Journal,2008,2(4):429-441.
[215] Lam P, Jensen MM, Lavik G, et al. Linking crenarchaeal and bacterial nitrification toanammox in the Black Sea[J]. Proceedings of the National Academy of Sciences of the UnitedStates of America,2007,104(17):7104-7109.
[216] Nakagawa T, Mori K, Kato C, et al. Distribution of cold-adapted ammonia-oxidizingmicroorganisms in the deep-ocean of the northeastern Japan Sea[J]. Microbes andEnvironments,2007,22(4):365-372.
[217] Coolen MJL, Abbas B, van Bleijswijk J, et al. Putative ammonia-oxidizing Crenarchaeota insuboxic waters of the Black Sea: a basin-wide ecological study using16S ribosomal andfunctional genes and membrane lipids[J]. Environmental Microbiology,2007,9(4):1001-1016.
[218] Park SJ, Park BJ, Rhee SK. Comparative analysis of archaeal16S rRNA and amoA genes toestimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments[J].Extremophiles,2008,12(4):605-615.
[219] Kalanetra KM, Bano N, Hollibaugh JT. Ammonia-oxidizing Archaea in the Arctic Ocean andAntarctic coastal waters[J]. Environmental Microbiology,2009.
[220] Beman JM, Roberts KJ, Wegley L, et al. Distribution and diversity of archaeal ammoniamonooxygenase genes associated with corals[J]. Applied and Environmental Microbiology,2007,73(17):5642-5647.
[221] Steger D, Ettinger-Epstein P, Whalan S, et al. Diversity and mode of transmission ofammonia-oxidizing archaea in marine sponges[J]. Environmental Microbiology,2008,10(4):1087-1094.
[222] Beman JM, Francis CA. Diversity of ammonia-oxidizing archaea and bacteria in thesediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico[J]. Applied andEnvironmental Microbiology,2006,72(12):7767-7777.
[223] Caffrey JM, Bano N, Kalanetra K, et al. Ammonia oxidation and ammonia-oxidizing bacteriaand archaea from estuaries with differing histories of hypoxia[J]. Isme Journal,2007,1(7):660-662.
[224] Santoro AE, Francis CA, de Sieyes NR, et al. Shifts in the relative abundance ofammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterraneanestuary[J]. Environmental Microbiology,2008,10(4):1068-1079.
[225] Weidler GW, Dornmayr-Pfaffenhuemer M, Gerbl FW, et al. Communities of Archaea andBacteria in a subsurface radioactive thermal spring in the Austrian Central Alps, and evidenceof ammonia-oxidizing Crenarchaeota[J]. Applied and Environmental Microbiology,2007,73(1):259-270.
[226] Pouliot J, Galand PE, Lovejoy C, et al. Vertical structure of archaeal communities and thedistribution of ammonia monooxygenase A gene variants in two meromictic High Arcticlakes[J]. Environmental Microbiology,2009,11(3):687-699.
[227] van der Wielen P, Voost S, van der Kooij D. Ammonia-Oxidizing Bacteria and Archaea inGroundwater Treatment and Drinking Water Distribution Systems[J]. Applied andEnvironmental Microbiology,2009,75(14):4687-4695.
[228] Park HD, Wells GF, Bae H, et al. Occurrence of ammonia-oxidizing archaea in wastewatertreatment plant bioreactors[J]. Applied and Environmental Microbiology,2006,72(8):5643-5647.
[229] Zhang T, Jin T, Yan Q, et al. Occurrence of ammonia-oxidizing Archaea in activated sludgesof a laboratory scale reactor and two wastewater treatment plants[J]. Journal of AppliedMicrobiology,2009,107(3):970-977.
[230] Wells GF, Park HD, Yeung CH, et al. Ammonia-oxidizing communities in a highly aeratedfull-scale activated sludge bioreactor: betaproteobacterial dynamics and low relativeabundance of Crenarchaea[J]. Environmental Microbiology,2009,11(9):2310-2328.
[231] Schleper C, Jurgens G, Jonuscheit M. Genomic studies of uncultivated archaea[J]. NatureReviews Microbiology,2005,3(6):479-488.
[232] Konneke M, Bernhard AE, de la Torre JR, et al. Isolation of an autotrophicammonia-oxidizing marine archaeon[J]. Nature,2005,437(7058):543-546.
[233] de la Torre JR, Walker CB, Ingalls AE, et al. Cultivation of a thermophilic ammonia oxidizingarchaeon synthesizing crenarchaeol[J]. Environmental Microbiology,2008,10(3):810-818.
[234] Hatzenpichler R, Lebecleva EV, Spieck E, et al. A moderately thermophilicammonia-oxidizing crenarchaeote from a hot spring[J]. Proceedings of the National Academyof Sciences of the United States of America,2008,105(6):2134-2139.
[235] Tourna M, Stieglmeier M, Spang A, et al. Nitrososphaera viennensis, an ammonia oxidizingarchaeon from soil[J]. Proceedings of the National Academy of Sciences of the United Statesof America,2011,108(20):8420-8425.
[236] Nicol GW, Leininger S, Schleper C, et al. The influence of soil pH on the diversity, abundanceand transcriptional activity of ammonia oxidizing archaea and bacteria[J]. EnvironmentalMicrobiology,2008,10(11):2966-2978.
[237] Mosier AC, Francis CA. Relative abundance and diversity of ammonia-oxidizing archaea andbacteria in the San Francisco Bay estuary[J]. Environmental Microbiology,2008,10(11):3002-3016.
[238] Sahan E, Muyzer G. Diversity and spatio-temporal distribution of ammonia-oxidizing Archaeaand Bacteria in sediments of the Westerschelde estuary[J]. FEMS Microbiology Ecology,2008,64(2):175-186.
[239] Herrmann M, Saunders AM, Schramm A. Effect of lake trophic status and rooted macrophyteson community composition and abundance of ammonia-oxidizing prokaryotes in freshwatersediments[J]. Applied and Environmental Microbiology,2009,75(10):3127-3136.
[240] Ye W, Liu X, Lin S, et al. The vertical distribution of bacterial and archaeal communities inthe water and sediment of Lake Taihu[J]. FEMS Microbiology Ecology,2009,70(2):107-120.
[241] Lee JHW, Wang ZY, Thoe W, et al. Integrated physical and ecological management of the EastRiver[J]. Sustainable and Safe Water Supplies,2007,7(2):81-91.
[242] Francis CA, Roberts KJ, Beman JM, et al. Ubiquity and diversity of ammonia-oxidizingarchaea in water columns and sediments of the ocean[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2005,102(41):14683-14688.
[243] Rotthauwe JH, Witzel KP, Liesack W. The ammonia monooxygenase structural gene amoAasa functional marker: molecular fine-scale analysis of natural ammonia-oxidizingpopulations[J]. Applied and Environmental Microbiology,1997,63(12):4704-4712.
[244] Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool[J]. J Mol Biol,1990,215(3):403-410.
[245] Huber T, Faulkner G, Hugenholtz P. Bellerophon: a program to detect chimeric sequences inmultiple sequence alignments[J]. Bioinformatics,2004,20(14):2317-2319.
[246] Schloss PD, Handelsman J. Introducing DOTUR, a computer program for defining operationaltaxonomic units and estimating species richness[J]. Applied and Environmental Microbiology,2005,71(3):1501-1506.
[247] Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetictrees[J]. Mol Biol Evol,1987,4(4):406-425.
[248] Okano Y, Hristova KR, Leutenegger CM, et al. Application of real-time PCR to study effectsof ammonium on population size of ammonia-oxidizing bacteria in soil[J]. Applied andEnvironmental Microbiology,2004,70(2):1008-1016.
[249] Chain P, Lamerdin J, Larimer F, et al. Complete genome sequence of the ammonia-oxidizingbacterium and obligate chemolithoautotroph Nitrosomonas europaea[J]. Journal ofBacteriology2003,185(9):2759-2773.
[250] Smil V, Yushi M. The economic costs of China's environmental degradation[M]. Beijing,China: American Academy of Arts and Sciences,1998.
[251] Bollmann A, Bar-Gilissen MJ, Laanbroek HJ. Growth at low ammonium concentrations andstarvation response as potential factors involved in niche differentiation amongammonia-oxidizing bacteria[J]. Applied and Environmental Microbiology,2002,68(10):4751-4757.
[252] Koops HP, Pommerening-Roser A. Distribution and ecophysiology of the nitrifying bacteriaemphasizing cultured species[J]. FEMS Microbiology Ecology,2001,37(1):1-9.
[253] Schramm A, de Beer D, van den Heuvel JC, et al. Microscale distribution of populations andactivities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifyingbioreactor: Quantification by in situ hybridization and the use of microsensors[J]. Applied andEnvironmental Microbiology,1999,65(8):3690-3696.
[254] Cavicchioli R, DeMaere MZ, Thomas T. Metagenomic studies reveal the critical andwide-ranging ecological importance of uncultivated archaea: the role of ammonia oxidizers[J].Bioessays,2007,29(1):11-14.
[255] Zhang T, Jin T, Yan Q, et al. Occurrence of ammonia-oxidizing Archaea in activated sludgesof a laboratory scale reactor and two wastewater treatment plants[J]. Journal of AppliedMicrobiology,2009.
[256] Erguder TH, Boon N, Wittebolle L, et al. Environmental factors shaping the ecological nichesof ammonia-oxidizing archaea[J]. FEMS Microbiology Reviews2009,33(5):855-869.
[257] Jiang HC, Dong HL, Yu BS, et al. Diversity and abundance of ammonia-oxidizing archaea andbacteria in Qinghai Lake, northwestern China[J]. Geomicrobiology Journal,2009,26(3):199-211.
[258] Martens-Habbena W, Berube PM, Urakawa H, et al. Ammonia oxidation kinetics determineniche separation of nitrifying Archaea and Bacteria[J]. Nature,2009,461(7266):976-U234.
[259] Park BJ, Park SJ, Yoon DN, et al. Cultivation of autotrophic ammonia-oxidizing archaea frommarine sediments in co-culture with sulfur-oxidizing bacteria[J]. Applied and EnvironmentalMicrobiology,2010,76(22):7575-7587.
[260] Tourna M, Freitag TE, Nicol GW, et al. Growth, activity and temperature responses ofammonia-oxidizing archaea and bacteria in soil microcosms[J]. Environmental Microbiology,2008,10(5):1357-1364.
[261] Church MJ, Wai B, Karl DM, et al. Abundances of crenarchaeal amoAgenes and transcripts inthe Pacific Ocean[J]. Environmental Microbiology,2010,12(3):679-688.
[262] Di HJ, Cameron KC, Shen JP, et al. Nitrification driven by bacteria and not archaea innitrogen-rich grassland soils[J]. Nature Geoscience,2009,2(9):621-624.
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |